Thymidine kinase mutants and fusion proteins having thymidine kinase and guanylate kinase activities

ABSTRACT

The present invention provides isolated nucleic acid molecules encoding a Herpesviridae thymidine kinase enzyme comprising one or more mutations, at least one of the mutations encoding an amino acid substitution located toward the N-terminus from a DRH nucleoside binding site which increases a biological activity of the thymidine kinase, as compared to unmutated thymidine kinase. Such mutations include amino acid substitutions within a Q substrate binding domain which increases a biological activity of the thymidine kinase, as compared to unmutated thymidine kinase. Within a further aspect, fusion proteins are provided which have both guanylate kinase and thymidine kinase biological properties. Also provided are vectors suitable for expressing such DNA molecules, as well as methods for utilizing such vectors.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.60/061,812, filed Oct. 14, 1997, which application is incorporated byreference in its entirety.

TECHNICAL FIELD

The present invention relates generally to mutant enzymes of theHerpesviridae and, more specifically, to compositions and methods whichutilize thymidine kinase mutants. The present invention also relates tofusion proteins having both guanylate kinase and thymidine kinaseactivities.

BACKGROUND OF THE INVENTION

Although many bacterial diseases are, in general, easily treated withantibiotics, very few effective treatments exist for many viral,parasitic, cancerous, and genetic diseases. Cancer, for example, may betreated by surgical resection of a solid tumor. Nevertheless, a majorityof patients with solid tumors also possess micrometastases beyond theprimary tumor site. If treated with surgery alone, approximately 70% ofthese patients will experience recurrence of the cancer. Thus, canceraccounts for one-fifth of the total mortality in the United States, andis the second leading cause of death.

In addition to surgery, many cancers are now also treated with acombination of therapies involving cytotoxic chemotherapeutic drugs(e.g., vincristine, vinblastine, cisplatin, methotrexate, 5-FU, etc.)and/or radiation therapy. One difficulty with this approach, however, isthat radiotherapeutic and chemotherapeutic agents are toxic to normaltissues, and often create life-threatening side effects. In addition,these approaches often have extremely high failure/remission rates (upto 90% depending upon the type of cancer).

Numerous other methods have been attempted in order to bolster oraugment an individual's own immune system in order to eliminate cancercells. For example, some scientists have utilized bacterial or viralcomponents as adjuvants, in order to stimulate the immune system todestroy tumor cells. Such agents have generally been useful as adjuvantsand as nonspecific stimulants in animal tumor models, but have not yetproved to be generally effective in humans.

Lymphokines have also been utilized in the treatment of cancer (as wellas viral and parasitic diseases), in order to stimulate or affectspecific immune cells in the generation of an immune response. Onegroup, for example, utilized the lymphokine Interleukin-2 in order tostimulate peripheral blood cells in order to expand and produce largequantities of cells which are cytotoxic to tumor cells (Rosenberg etal., N. Engl. J. Med. 313:1485-1492, 1985).

Others have suggested the use of antibody-mediated treatment usingspecific monoclonal antibodies or “magic bullets” in order tospecifically target and kill tumor cells (Dillman, “Antibody Therapy,”Principles of Cancer Biotherapy, Oldham (ed.), Raven Press, Ltd., NewYork, 1987). One difficulty, however, is that most monoclonal antibodiesare of murine origin, and thus hypersensitivity against the murineantibody may limit its efficacy, particularly after repeated therapies.Common side effects include fever, sweats and chills, skin rashes,arthritis, and nerve palsies.

One approach which has recently garnered significant interest is the useof gene therapy, which has been utilized to treat not only geneticdiseases, but viral and cancerous diseases as well (see PCT PublicationNos. WO 91/02805, EPO 415,731, and WO 90/07936). Briefly, specificallydesigned vectors which have been derived from viruses are used todeliver particular genetic information into cells. Such geneticinformation may itself be useful to block expression of damagingproteins or antigens (e.g., antisense therapy), may encode proteinswhich are toxic and kill selected cells, may encode therapeutic proteinswhich bolster a cell's immune response, or encode protein's whichreplace inactive or nonexistent proteins.

One protein which has recently been suggested for use in such therapiesis the type 1 Herpes Simplex Virus thymidine kinase (HSVTK-1). Briefly,thymidine kinase is a salvage pathway enzyme which phosphorylatesnatural nucleoside substrates as well as nucleoside analogues (seeBalasubramaniam et al., J. of Gen. Vir. 71:2979-2987, 1990). Thisprotein may be utilized therapeutically by introducing a retroviralvector which expresses the protein into the cell, followed byadministration of a nucleoside analogue such as acyclovir organciclovir. HSVTK-1 then phosphorylates the nucleoside analogue,creating a toxic product capable of killing the host cell. Thus, use ofretroviral vectors which express HSVTK has been suggested for not onlythe treatment of cancers, but for other diseases as well.

The present invention provides novel thymidine kinase mutants and TKfusion proteins with enhanced biological activities which are suitablefor a variety of applications, such as gene therapy, and furtherprovides other, related advantages.

SUMMARY OF THE INVENTION

Briefly stated, the present invention provides compositions and methodswhich utilize Herpesviridae thymidine kinase mutants. Within one aspectof the present invention, isolated nucleic acid molecules which encodeHerpesviridae thymidine kinase enzymes comprising one or more mutationsare provided, wherein at least one of the mutations encoding an aminoacid substitution is positioned within the Q substrate binding domain,wherein the mutation increases a biological activity of the thymidinekinase, as compared to unmutated thymidine kinase. Within another aspectof the present invention, isolated nucleic acid molecules are providedencoding a Herpesviridae thymidine kinase enzyme comprising at leastthree mutations, at least two of the mutations being amino acidsubstitutions located toward the N-terminus from a DRH nucleosidebinding site (e.g., 1, 2 or 3 amino acids toward the N-terminus), and atleast one mutation located toward the C-terminus from a DRH nucleosidebinding site (e.g., 4 or 5 amino acids toward the C-terminus) whichincreases a biological activity of the thymidine kinase, as compared tounmutated thymidine kinase. Representative examples of suitableHerpesviridae thymidine kinase enzymes include Herpes Simplex Virus Type1 thymidine kinase, Herpes Simplex Virus Type 2 thymidine kinase,Varicella Zoster Virus thymidine kinase, and marmoset herpesvirus,feline herpesvirus type 1, pseudorabies virus, equine herpesvirus type1, bovine herpesvirus type 1, turkey herpesvirus, Marek's disease virus,herpesvirus saimiri and Epstein-Barr virus thymidine kinases. Withinother embodiments, the thymidine kinase may be a primate herpesvirusthymidine kinase, or a non-primate herpesvirus thymidine kinase, such asan avian herpesvirus thymidine kinase.

A wide variety of mutations are contemplated within the context of thepresent invention. For example, within one embodiment mutations, such asamino acid substitutions, may occur within a region that includes the Qsubstrate binding domain and an additional 11 amino acids from thisdomain, toward the N-terminus.

In other embodiments, at least one mutation occurs within this“expanded” Q substrate binding domain or within the Q substrate bindingdomain, and at least one mutation is present outside these two regions.For example, one or more additional mutations may be located within aDRH nucleoside binding site which increases a biological activity ofsaid thymidine kinase, as compared to unmutated thymidine kinase. Forexample, glutamic acid may be substituted for aspartic acid in the DRHnucleoside binding site, or a histidine residue may be substituted forarginine in the DRH nucleoside binding site.

Within yet another aspect, isolated nucleic acid molecules are providedencoding a Herpesviridae thymidine kinase enzyme comprising at least onemutation, such as an amino acid substitution, within a Q substratebinding domain (or within an expanded Q substrate binding domain) and atleast one additional mutation being an amino acid substitution locatedtoward the C-terminus from a DRH nucleoside binding site (e.g., 4, 5 or6 amino acids toward the C-terminus) which increases a biologicalactivity of the thymidine kinase, as compared to unmutated thymidinekinase.

Alternatively, additional mutations may encode one or more amino acidsubstitutions located from 1 to 7 amino acids toward the N-terminus fromthe DRH nucleoside binding site. For example, the amino acid which isone position toward the N-terminus from the DRH nucleoside binding siteis substituted with an amino acid selected from the group consisting ofvaline, leucine, cysteine and isoleucine. Within another embodiment, theamino acid alanine is substituted for the amino acid which is presentseven amino acids toward the N-terminus from the DRH nucleoside bindingsite. Within other embodiments, the thymidine kinase enzyme istruncated, and yet retains biological activity.

Within further embodiments of the invention, isolated nucleic acidmolecules are provided which encode a thymidine kinase enzyme capable ofphosphorylating a nucleoside analogue (e.g., acyclovir or ganciclovir)at least one-fold over the phosphorylation of the nucleoside analogue bya wild-type thymidine kinase enzyme. Within other embodiments, thethymidine kinase enzyme phosphorylates a nucleoside analogue at leastx-fold over the phosphorylation of a nucleoside analogue by a wild-typethymidine kinase enzyme, wherein x is selected from the group consistingof 1.5, 2, 2.5, 3, 3.5, 4, 4.5 and 5. Within yet another embodiment, thethymidine kinase enzyme is capable of phosphorylating a nucleosideanalogue, wherein

$z < \left\lbrack \frac{\left. {({TKmNAp})/{TKmTp}} \right)}{({TKwtNAp})/({TKwtTp})} \right\rbrack$

and wherein TK_(m) NA_(p) is the rate of phosphorylation of a nucleosideanalogue by a thymidine kinase mutant, TK_(m) T_(p) is the rate ofphosphorylation of thymidine by a thymidine kinase mutant, TK_(wt)NA_(p) is the rate of phosphorylation of a nucleoside analogue by anunmutated thymidine kinase enzyme, TK_(wt) T_(p) is the rate ofphosphorylation of a thymidine kinase enzyme by an unmutated thymidinekinase enzyme, and z is selected from the group consisting of 1, 1.5, 2,2.5, 3, 3.5, 4, 4.5 and 5. Representative examples of suitablenucleoside analogues include ganciclovir, acyclovir, famciclovir,buciclovir, penciclovir, valciclovir, trifluorothymidine, 1-[2-deoxy,2-fluoro, beta-D-arabino furanosyl]-5-iodouracil, ara-A, araT1-beta-D-arabinofuranoxyl thymine, 5-ethyl-2′-deoxyuridine,5-iodo-5′-amino-2,5′-dideoxyuridine, idoxuridine, AZT, AIU,dideoxycytidine and AraC.

Particularly preferred mutant thymidine kinases for the increasedphosphorylation of nucleoside analogues include those wherein the enzymeis a type 1 Herpes Simplex Virus thymidine kinase.

Within other aspects of the present invention, mutant thymidine kinaseenzymes which are encoded by the above-described nucleic acid moleculesare provided, as well as vectors which are capable of expressing suchmolecules. Within one aspect, expression vectors are provided comprisinga promoter operably linked to a nucleic acid molecule of the presentinvention. Within a preferred aspect, the vector is a viral vectorcapable of directing the expression of a nucleic acid molecule asdescribed above. Representative examples of such viral vectors includeherpes simplex viral vectors, adenoviral vectors, adenovirus-associatedviral vectors, pox vectors, parvoviral vectors, baculovirus vectors andretroviral vectors. Within another aspect, viral vectors are providedwhich are capable of directing the expression of a nucleic acid moleculewhich encodes a thymidine kinase enzyme comprising one or moremutations, at least one of the mutations encoding an amino acidsubstitution which increases a biological activity of thymidine kinase,as compared to unmutated thymidine kinase.

A wide variety of promoters may be utilized in the present invention,including, for example, promoters such as the MoMLV LTR, RSV LTR, FriendMuLv LTR, Adenoviral promoter, Neomycin phosphotransferasepromoter/enhancer, late parvovirus promoter, Herpes TK promoter, SV40promoter, Metallothionen IIa gene enhancer/promoter, CytomegalovirusImmediate Early Promoter, Cytomegalovirus Immediate Late Promoter, aswell as tissue-specific promoters such as the tyrosinase relatedpromoters (TRP-1 and TRP-2), DF3 enhancer, SLPI promoter (secretoryleucoprotease inhibitor—expressed in many types of carcinomas), TRS(tissue specific regulatory sequences), tyrosine hydroxylase promoter,adipocyte P2 promoter, PEPCK promoter, CEA promoter, α fetoproteinpromoter, whey acidic promoter, and casein promoter. Within relatedaspects, the above-described vectors may be provided as pharmaceuticalcompositions, along with a pharmaceutically acceptable carrier ordiluent.

The present invention further provides nucleic acid molecules encodingfusion proteins that comprise a thymidine kinase moiety and a guanylatekinase moiety. Such fusion proteins possess biological activities ofboth thymidine kinase and guanylate kinase. The thymidine kinase moietymay derived from a wild-type thymidine kinase or from one of thethymidine kinase mutants described herein.

Within further aspects, sequences which encode thymidine kinase mutants,thymidine kinase fusion proteins, or fusion proteins having guanylatekinase and thymidine kinase activities described herein may be includedwithin a given vector which is utilized for the purposes of genetherapy. Cells which contain these vectors may subsequently be killed byadministration of a nucleoside analogue, in order to prevent formationof replication competent virus or aberrant integration of the vectorinto the host cell. Such compositions or methods are referred to as“suicide vectors” or a “failsafe” approach to gene therapy.

Within other aspects of the present invention, host cells are providedwhich carry one of the above-described vectors. Representative examplesof such cells include human cells, dog cells, monkey cells, rat cells,and mouse cells.

Within other aspects of the present invention, methods are provided forinhibiting a pathogenic agent in a warm-blooded animal, comprising thestep of administering to a warm-blooded animal a vector as describedabove, such that the pathogenic agent is inhibited. Within variousembodiments, the vector may be administered in vivo, or to cells exvivo, which are then transplanted (or re-transplanted) in the animal.Within other embodiments, the pathogenic agent may be viruses, bacteria,parasites, tumor cells, or autoreactive immune cells.

Within other aspects of the present invention, methods are provided fornoninvasive monitoring of the activity of herpes virus thymidine kinaseactivity, such as for the monitoring of the progress of gene therapyusing herpes virus thymidine kinase. According to such methods, asubject, who has received a vector comprising a herpes virus thymidinekinase, is scanned (e.g., using a clinical gamma camera or bysinglephoton emission tomography) for radiolabeled anti-viral drugs thatare substrates for the thymidine kinase.

These and other aspects of the present invention will become evidentupon reference to the following detailed description and attacheddrawings. In addition, various references are set forth below whichdescribe in more detail certain procedures or compositions (e.g.,plasmids, etc.), and are therefore incorporated by reference in theirentirety.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic outline which depicts a strategy for constructionof a random nucleotide-containing library, and selection of TK mutants.

FIG. 2 is a photograph which shows selection of TK and AZT mutants.

FIG. 3 depicts the nucleic acid and amino acid sequences of Wildtype,TKF 105, TK1208, and ATKF2 TK for codons 165 to 175.

FIG. 4 is a series of graphs which depict the thermostability ofwildtype TK and TK mutants.

FIG. 5 is a graph which depicts heat-inactivation profiles for in vitrotranslated wild-type and TKF2 thymidine kinase.

FIG. 6 is an autoradiograph of SDS/PAGE-fractionated in vitro translatedproducts (wild-type and TKF2).

FIG. 7 is an autoradiograph of ³⁵S-radiolabeled cell-free translationproducts subjected to SDS-PAGE and TCA-precipitable counts.

FIGS. 8A and 8B are two graphs which illustrate a time course analysisof high activity (A) and low activity (B) mutants produced in a rabbitreticulocyte lysate cell-free translation system.

FIGS. 9A and 9B are two graphs which show the thermal stability of highactivity (A) and low activity (B) TK mutants.

FIG. 10 is a bar graph which depicts a phosphorylation of nucleosidesand nucleoside analogs by mutant and wild-type thymidine kinases.

FIG. 11 is a bar graph which indicates TK activity of wild-type, TKF36,and dummy (pMDC) plasmids.

FIG. 12 is a graph which indicates the thymidine uptake activity ofcells containing TKF36, TKF52, wild-type plasmid, TKF99, or dummyplasmids (pMDC) over time.

FIG. 13 is a schematic illustration of one representative example ofgene therapy utilizing an HSVTK mutant.

FIG. 14 is an illustration which depicts the nucleotides which wererandomized in the LIF-ALL library, as well as the results of selection.

FIG. 15 is a table which shows amino acid substitutions of selected andunselected clones.

FIG. 16 is a table which shows the number of mutants selected from theLIF-ALL library which were sensitive to GCV or ACV.

FIG. 17 is a table which shows nucleotide changes in selected TKmutants.

FIG. 18 is a table which shows the amino acid sequence at positions159-161 and 168-170, and phosphorylation level of several mutant TKs.

FIG. 19 is a graph which shows the survival of cells grown on GCV andtransfected with various TK mutants.

FIG. 20 is a graph which shows the survival of cells grown on ACV andtransfected with various TK mutants.

FIG. 21 shows semi-randomized olignucleotides used to generate a secondgeneration of TK mutants having amino acid substitutions in residues159-161 and 168-169.

FIG. 22 illustrates the use of particular oligonucleotides to constructTK mutants having amino acid substitutions in residues 112-132.

FIG. 23 shows nucleotides in the open reading frame of HSVTK-1 (SEQUENCEID No. 1).

FIG. 24 illustrates a nucleotide sequence and deduced amino acidsequence representative of a human guanylate kinase.

FIG. 25 illustrates a nucleotide sequence and deduced amino acidsequence of a representative murine guanylate kinase.

FIG. 26 is a graph which shows the sensitivity of TK clones to GCV.

FIG. 27 is a graph which shows the sensitivity of TK clones to ACV.

FIG. 28 is a graph which shows the sensitivity of guanylate kinasetransfectant pools to GCV in TK expressing clones.

FIG. 29 is a graph which shows the sensitivity of guanylate kinasetransfectant pools to ACV in TK expressing clones.

FIG. 30 is an illustration of gmk/TK fusion protein constructs.

FIG. 31 is a graph which shows a ganciclovir dose response curve,comparing wild-type TK with a gmk/TK fusion protein.

FIG. 32 is a graph which shows tumor growth after transfection byvarious vectors, and subsequent exposure to ACV.

FIG. 33 is a graph which shows tumor growth after transfection byvarious vectors, and subsequent exposure to GCV.

FIG. 34 is a bar graph which shows the percentage change of tumor weightfor various treatments.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Prior to setting forth the invention, it may be helpful to anunderstanding thereof to first set forth definitions of certain termsthat will be used hereinafter.

“Vector” refers to an assembly which is capable of directing theexpression of the mutant tk gene, as well as any additional sequence(s)or gene(s) of interest. The vector must include transcriptionalpromoter/enhancer elements, as well as another sequence which, whentranscribed, is operably linked to the tk gene and/or other gene ofinterest. The vector may be composed of either deoxyribonucleic acids(“DNA”), ribonucleic acids (“RNA”), or a combination of the two (e.g., aDNA-RNA chimeric). Optionally, the vector may include a polyadenylationsequence, one or more restriction sites, as well as one or moreselectable markers such as neomycin phosphotransferase or hygromycinphosphotransferase. Additionally, depending on the host cell chosen andthe vector employed, other genetic elements such as an origin ofreplication, additional nucleic acid restriction sites, enhancers,sequences conferring inducibility of transcription, and selectablemarkers, may also be incorporated into the vectors described herein.

“Tissue-specific promoter” refers to transcriptional promoter/enhancerelements which control gene expression in a limited number of tissues,or in a single tissue. Representative examples of tissue-specificpromoters include the tyrosine hydroxylase promoter, adipocyte P2promoter, PEPCK promoter, α fetoprotein promoter, whey acidic promoter,and casein promoter.

“Biological activity of thimidine kinase” refers to the ability of thethymidine kinase enzyme to phosphorylate nucleosides (e.g., dT) andnucleoside analogues such as ganciclovir(9-{[2-hydroxy-1-(hydroxymethyl)ethoxyl methyl}guanosine), famciclovir,buciclovir, penciclovir, valciclovir, acyclovir (9-[2-hydroxyethoxy)methyl]guanosine), trifluorothymidine, 1-[2-deoxy, 2-fluoro,beta-D-arabino furanosyl]-5-iodouracil, ara-A (adenosine arabinoside,vivarabine), 1-beta-D-arabinofuranoxyl thymine, 5-ethyl-2′-deoxyuridine,5-iodo-5′-ammo-2,5′-dideoxyuridine, idoxuridine(5-iodo-2′-deoxyuridine), AZT (3′ azido-3′ thymidine), ddC(dideoxycytidine), AIU (5-iodo-5′ amino 2′,5′-dideoxyuridine) and AraC(cytidine arabinoside). As utilized herein, a thymidine kinase mutant isconsidered to have “increased biological activity” if the level or rateof activity increases at least “y” fold over unmutated thymidine kinase,wherein y is selected from the group consisting of 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5 and 5. Within preferred embodiments, thymidine kinasemutants are considered to have increased biological activity when

$z < \left\lbrack \frac{\left. {({TKmNAp})/{TKmTp}} \right)}{({TKwtNAp})/({TKwtTp})} \right\rbrack$

wherein TK_(m) NA_(p) is the rate of phosphorylation of a nucleosideanalogue by a thymidine kinase mutant, TK_(m) T_(p) is the rate ofphosphorylation of thymidine by a thymidine kinase mutant, TK_(m) NA_(p)is the rate of phosphorylation of a nucleoside analogue by an unmutatedthymidine kinase enzyme, TK_(m) T_(p) is the rate of phosphorylation ofa thymidine kinase enzyme by an unmutated thymidine kinase enzyme, and zis selected from the group consisting of 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5and 5.

“Biological activity of guanylate kinase” refers to the ability of theguanylate kinase enzyme to catalyze the reversible transfer of theterminal phosphoryl group of ATP to an acceptor molecule such as GMP ordGMP. Guanylate kinase (gmk) can also phosphorylate nucleosides andnucleoside analogs that have been phosphorylated by thymidine kinase.Examples of thymidine kinase substrates are described above.

In addition to the ability of thymidine kinase and guanylate kinase tophosphorylate nucleosides and nucleoside analogues, the phrase“biological activity” should also be understood to refer to otherbiological properties of these enzymes, such as protein stability (e.g.,as measured by resistance to proteolytic enzyme degradation by enzymessuch as trypsin), and thermostability (e.g., maintenance of nucleosideanalogue phosphorylation upon increases in temperature).

“Pathogenic agent” refers to either a foreign organism which isresponsible for a disease state, or an “altered” cell which isresponsible for a disease state. Representative examples of pathogenicagents include foreign organisms such as viruses, bacteria andparasites, as well as altered cells such as tumor cells and autoreactiveimmune cells. As utilized herein, a pathogenic agent is considered to be“inhibited” if either the growth or spread of the pathogenic agent isslowed, or if the pathogenic agent itself is destroyed.

As noted above, the present invention provides compositions and methodswhich utilize Herpesviridae thymidine kinase mutants. Briefly, thymidinekinase mutants of the present invention may be prepared from a widevariety of Herpesviridae thymidine kinases, including for example bothprimate herpesviruses, and nonprimate herpesviruses such as avianherpesviruses. Representative examples of suitable herpesviruses includeHerpes Simplex Virus Type 1 (McKnight et al., Nuc. Acids Res8:5949-5964, 1980), Herpes Simplex Virus Type 2 (Swain and Galloway, J.Virol. 46:1045-1050, 1983), Varicella Zoster Virus (Davison and Scott,J. Gen. Virol. 67:1759-1816, 1986), marmoset herpesvirus (Otsuka andKit, Virology 135:316-330, 1984), feline herpesvirus type 1 (Nunberg etal., J. Viral. 63:3240-3249, 1989), pseudorabies virus (Kit and Kit,U.S. Pat. No. 4,514,497, 1985), equine herpesvirus type 1 (Robertson andWhalley, Nuc. Acids Res. 16:11303-11317, 1988), bovine herpesvirus type1 (Mittal and Field, J. Virol 70:2901-2918, 1989), turkey herpesvirus(Martin et al., J. Virol. 63:2847-2852, 1989), Marek's disease virus(Scott et al., J. Gen. Virol. 70:3055-3065, 1989), herpesvirus saimiri(Honess et al., J. Gen. Virol. 70:3003-3013, 1989) and Epstein-Barrvirus (Baer et al., Nature (London) 310:207-311, 1984).

Such herpesviruses may be readily obtained from commercial sources suchas the American Type Culture Collection (“ATCC”, Rockville, Md.).Deposits of certain of the above-identified herpesviruses may be readilyobtained from the ATCC, for example: ATCC No. VR-539 (Herpes simplextype 1); ATCC Nos. VR-734 and VR-540 (Herpes Simplex type 2); ATCC No.VR-586 (Varicella Zoster Virus); ATCC No. VR-783 (Infectiouslaryngothracheitis); ATCC Nos. VR-624 VR-987, VR-2103, VR-2001, VR-2002,VR-2175, VR-585 (Marek's disease virus); ATCC Nos. VR-584B and VR-584B(turkey herpesvirus); ATCC Nos. VR-631 and VR-842 (bovine herpesvirustype 1); and ATCC Nos. VR-2003, VR-2229 and VR-700 (equine herpesvirustype 1). Herpesviruses may also be readily isolated and identified fromnaturally occurring sources (e.g., from an infected animal).

Any of the above-cited herpesviruses (as well as other members of theHerpesviridae) may be readily utilized in order to prepare thymidinekinase mutants of the present invention. Briefly, one primary regionwhich is believed to be responsible for nucleoside binding is found inthe area surrounding Sites 3 and 4 (see Balasubramaniam et al., J. Gen.Vir. 71:2979-2987, 1990). These sites are characterized by highlyconserved regions, and consist of the motif -DRH- (for Site 3), and-C(Y/F)P- (for Site 4). Although the numbering of nucleic acids maychange substantially from one herpesvirus to another, as utilizedherein, reference will be made to positions relative to the DRHnucleoside binding site. For example, for Herpes Simplex Virus type 1(McKnight et al., Nucl. Acids Res. 8:5949-5964, 1980), this site may befound at amino acids 162, 163 and 164. DRH nucleoside binding sites forother representative herpesviruses include: 163, 164 and 165 for HerpesSimplex Virus type 2; 129, 130 and 131 for Varicella Zoster Virus; 130,131 and 132 for Marmoset herpesvirus; and 148, 149 and 150 forEpstein-Barr virus.

For herpesviruses which have not been previously sequenced, the DRHnucleoside binding site may be readily identified by sequencing thenucleic acid sequence encoding the enzyme, or by amino acid sequencingthe enzyme itself, followed by alignment of the sequence to other knownherpesvirus sequences (see Balasubramanian, ibid.). To the extent thatmore than one -DRH- motif is identified, the proper motif may be readilyidentified by, for example, crystal structure analysis (Sanderson etal., J. Mol. Biol. 202:917-919, 1988; Montfort et al., Biochem29(30):6964-6977, 1990; Hardy et al., Science 235:448-455, 1987), orcrosslinking studies (Knoll et al., Bioch. Biophys. Acta 1121:252-260,1992).

The thymidine kinase gene from the selected herpesvirus may then bereadily isolated and mutated as described below, in order to constructnucleic acid molecules encoding a thymidine kinase enzyme comprising oneor more mutations which increases a biological activity of the thymidinekinase, as compared to unmutated thymidine kinase. As utilized herein,it should be understood that “unmutated thymidine kinase” refers tonative or wild-type thymidine kinase such as that described by McKnightet al. (Nucl. Acids Res. 8:5949-5964, 1980). The biological activity ofsuch kinases may be readily determined utilizing any of the assays whichare described herein, including for example, determination of the rateof nucleoside analogue uptake, determination of the rate of nucleosideor nucleoside analogue phosphorylation (see Examples 2-4). In addition,thymidine kinase mutants may be readily selected which are characterizedby other biological properties, such as thermostability (see Examples2-4), and protein stability.

A wide variety of thymidine kinase mutations are contemplated within thescope of the present invention. For example, within one embodiment ofthe invention, isolated nucleic acid molecules are provided which encodea Herpesviridae thymidine kinase enzyme comprising one or moremutations, at least one of the mutations encoding an amino acidsubstitution located toward the N-terminus from the DRH nucleosidebinding site. Briefly, any amino acid position toward the N-terminus ofthe DRH nucleoside binding site may be substituted for another aminoacid given the disclosure provided herein. Representative amino acidswhich may be substituted (and their one letter symbols) include alanine(A), arginine (R), asparagine (N), aspartic acid (D), cysteine (C),glutamine (Q), glutamic acid (E), glycine (G), histidine (H), isoleucine(I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline(P), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine(V).

For example, within one embodiment of the invention, isolated nucleicacid molecules are provided which encode a Herpesviridae thymidinekinase enzyme comprising at least three mutations, at least two of themutations being amino acid substitutions located toward the N-terminusfrom a DRH nucleoside binding site (e.g., 1, 2 or 3 amino acids towardthe N-terminus), and at least one mutation located toward the C-terminusfrom a DRH nucleoside binding site (e.g., 4 or 5 amino acids toward theC-terminus) which increases a biological activity of the thymidinekinase, as compared to unmutated thymidine kinase. Briefly, an aminoacid in any of these positions may be substituted for another amino acidgiven the disclosure provided herein. Representative amino acids whichmay be substituted (and their one letter symbols) include alanine (A),arginine (R), asparagine (N), aspartic acid (D), cysteine (C), glutamine(Q), glutamic acid (E), glycine (G), histidine (H), isoleucine (I),leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P),serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V).With reference to TK mutants having at least two mutations toward theN-terminus and at least one mutation toward the C-terminus from a DRHsite, preferred amino acids that may be substituted for amino acids of awild-type sequence include alanine (A), asparagine (N), isoleucine (I),leucine (L), methionine (M), phenylalanine (F), tyrosine (Y), and valine(V).

Within another embodiment of the invention, nucleic acid molecules areprovided which encode thymidine kinase mutants either with one or moreamino acid substitutions within the Q substrate binding domain, or withone or more amino acid substitutions within an expanded region thatincludes the Q substrate binding domain and an additional 11 amino acidresidues located toward the N-terminus (“the expanded Q substratebinding domain”). Representative amino acids which may be substituted(and their one letter symbols) include alanine (A), arginine (R),asparagine (N), aspartic acid (D), glutamine (Q), glutamic acid (E),glycine (G), histidine (H), lysine (K), methionine (M), phenylalanine(F), proline (P), serine (S), threonine (T), tryptophan (W), andtyrosine (Y).

Within another embodiment, nucleic acid molecules are provided whichencode thymidine kinase mutants having with one or more amino acidsubstitutions within the Q substrate binding domain or within theexpanded Q substrate binding domain, and at least one additional aminoacid substitution located from two to six positions toward theN-terminus from the DRH nucleoside binding site. Representative aminoacids which may be substituted include alanine (A), arginine (R),asparagine (N), aspartic acid (D), cysteine (C), glutamine (Q), glutamicacid (E), glycine (G), histidine (H), isoleucine (I), leucine (L),lysine (K), methionine (M), phenylalanine (F), proline (P), serine (S),threonine (T), tryptophan (W), tyrosine (Y), and valine (V).

Within other embodiments, nucleic acid molecules are provided whichencode thymidine kinase mutants having with one or more amino acidsubstitutions within the Q substrate binding domain or within theexpanded Q substrate binding domain, and at least one additional aminoacid substitution located seven positions toward the N-terminus from theDRH nucleoside binding site. Representative amino acids which may besubstituted include arginine (R), asparagine (N), aspartic acid (D),cysteine (C), glutamine (Q), glutamic acid (E), glycine (G), histidine(H), isoleucine (I), leucine (L), lysine (K), methionine (M),phenylalanine (F), proline (P), serine (S), threonine (T), tryptophan(W), tyrosine (Y), and valine (V).

Within other aspects of the invention, nucleic acid molecules areprovided which encode thymidine kinase mutants having with one or moreamino acid substitutions within the Q substrate binding domain or withinthe expanded Q substrate binding domain, and at least one additionalmutation, as described by Dedieu et al., international publication No.WO 95/14102, which is hereby incorporated by reference.

Within another aspect of the present invention, nucleic acid moleculesare provided which encode thymidine kinase mutants having with one ormore amino acid substitutions within the Q substrate binding domain orwithin the expanded Q substrate binding domain, and at least oneadditional amino acid substitution within the DRH nucleoside bindingsite. Within one embodiment of the invention, the asparatic acid in theDRH nucleoside binding site is substituted with other amino acids,including for example, alanine (A), arginine (R), asparagine (N),cysteine (C), glutamine (Q), glutamic acid (E), glycine (G), histidine(H), isoleucine (I), leucine (L), lysine (K), methionine (M),phenylalanine (F), proline (P), serine (S), threonine (T), tryptophan(W), tyrosine (Y), and valine (V). Within another embodiment of theinvention, the arginine in the DRH nucleoside binding site issubstituted with other amino acids, including for example, alanine (A),asparagine (N), aspartic acid (D), cysteine (C), glutamine (Q), glutamicacid (E), glycine (G), histidine (H), isoleucine (I), leucine (L),lysine (K), methionine (M), phenylalanine (F), proline (P), serine (S),threonine (T), tryptophan (W), tyrosine (Y), and valine (V).

Within other aspects of the present invention, nucleic acid moleculesare provided which encode thymidine kinase enzymes comprising two ormore mutations which increase a biological activity of the thymidinekinase enzyme, wherein the mutants have one or more amino acidsubstitutions within the Q substrate binding domain or within theexpanded Q substrate binding domain, and one or more amino acidsubstitutions located 1, 2 or 3 amino acids toward the N-terminus fromthe DRH nucleoside binding site, and/or one or more substitutionslocated 4, 5 or 6 amino acids toward the C-terminus from the DRHnucleoside binding site, or located 1, 2 or 3 amino acids toward theN-terminus from the CYP nucleoside binding site (see FIG. 14).

Within yet another embodiment of the invention, thymidine kinase mutantsare characterized by having one or more amino acid substitutions withinthe Q substrate binding domain or within the expanded Q substratebinding domain, and by having the histidine in the DRH nucleosidebinding site substituted with any other amino acid, including forexample, alanine (A), arginine (R), asparagine (N), aspartic acid (D),cysteine (C), glutamine (Q), glutamic acid (E), glycine (G), isoleucine(I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline(P), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine(V).

Within other aspects of the present invention, nucleic acid moleculesare provided which encode thymidine kinase enzymes comprising two ormore mutations which increase a biological activity of the thymidinekinase enzyme, wherein one or more amino acid substitutions are locatedwithin the Q substrate binding domain or within the expanded Q substratebinding domain, and wherein at least one mutation encodes an amino acidsubstitution located from 1 to 11 positions toward the C-terminus fromthe DRH nucleoside binding site. These amino acids may be substitutedwith other amino acids, including for example, alanine (A), arginine(R), asparagine (N), aspartic acid (D), cysteine (C), glutamine (Q),glutamic acid (E), glycine (G), histidine (H), isoleucine (I), leucine(L), lysine (K), methionine (M), phenylalanine (F), proline (P), serine(S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V).

Within another aspect of the present invention, nucleic acid moleculesare provided which encode thymidine kinase enzymes comprising one ormore mutations which increase a biological activity of the thymidinekinase enzyme, wherein one or more amino acid substitutions are locatedwithin the Q substrate binding domain or within the expanded Q substratebinding domain, and wherein at least one mutation encodes an amino acidsubstitution located from 12 to “v” positions toward the C-terminus fromthe DRH nucleoside binding site, wherein “v” is any integer greater than13 (and generally less than 202). These amino acids may be readilysubstituted with other amino acids, including for example, alanine (A),arginine (R), asparagine (N), aspartic acid 04 cysteine (C), glutamine(Q), glutamic acid (E), glycine (G), histidine (H), isoleucine (I),leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P),serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V).

Within various aspects, nucleic acid molecules of the present inventionmay encode several amino acid mutations. For example, within onepreferred embodiment, thymidine kinase mutants are provided which encodemutations with 1, 2, 3, 4, 5 or more amino acid substitutions, as wellas in-frame deletions. Example of such mutants include P155A/F161V,P155A/F161C, P155A/D162E, I160L/F161L/A168V/L169M andF161L/A168V/L169Y/L170C.

As described herein, mutagenesis of nucleotides encoding the residuessurrounding Sites 3 and 4 of HSV-1 TK has lead to improvements in thekinetic parameters (Km) towards nucleoside prodrugs. A new and distinctregion has been recently identified to participate in nucleoside bindingthat resides within amino acid residues 112-132. The region encodingresidues 112-132 of HSV-1 TK was implicated in substrate (or dTMP)binding by photoaffinity labeling using a 32P-azido-dUMP probe (Rechtinet al., Anal. Biochem. 237:135-140, 1996). This initial identificationwas supported by the observed proximity of these residues to boundsubstrate (thymidine or ganciclovir), as determined by X-raycrystallography studies (Wild et al., FEBS Lett. 368:289-292, 1995;Brown et al., Nature Struct. Biol. 2:876-881, 1995). Since the glutamine(“Q”) residue shows significant conservation in TK enzymes from a widevariety of sources (see, for example, Balasubramaniam et al., J. Gen.Virol. 71:2979-2987, 1990), the region of amino acid residues 112-132 isdesignated as the “Q substrate binding domain.”

Due to its role in substrate binding, this region is an excellent targetfor mutagenizing and selecting clones with altered substratespecificities. Such mutants would improve the efficacy and specificityof suicide gene therapy in the presence of specific prodrugs. Moreover,these mutant enzymes can be used for cell lineage ablation, restenosisand selection of homologous recombinants.

Accordingly, the present invention includes nucleic acid moleculesencoding forms of TK with at least one mutation within the Q substratebinding domain. The present invention also includes nucleic acidmolecules encoding truncated TK enzymes having at least one mutationwithin the Q substrate binding domain. The present invention furtherincludes mutant TK-encoding nucleic acid molecules with at least onemodification in a subregion of the Q substrate binding domain, such aswithin amino acid residues 123-132, or with at least one mutation in anexpanded region that includes the Q substrate binding domain and about11 additional amino acids toward the N-terminus, (e.g., within aminoacid residues 101-132). As an illustration, Example 10 describes methodsfor the mutagenesis of the region encoding amino acids 112-132 of HSV-1TK. In this example, TK mutants were constructed that contained 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21mutations within amino acid residues 112-132.

Identification of the Q substrate binding domain, which is distinct fromthe DRH nucleoside binding site, enables the construction of numerousthymidine kinase mutations. Such TK mutants include those having aminoacid substitutions in the Q substrate binding domain with any of thefollowing representative amino acids: alanine, arginine, asparagine,aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine,isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine,threonine, tryptophan, tyrosine, and valine. Functionally, TK mutantshaving an alteration in the Q substrate binding domain are characterizedby an increased biological activity of thymidine kinase, as comparedwith unmutated thymidine kinase.

Although Example 10 illustrates mutagenesis of the HSV-1 TK Q substratebinding domain, the present invention also includes a variety ofthymidine kinase mutants having alterations in this domain.Identification of a Q substrate binding domain in various TK enzymes canbe achieved by aligning a TK amino acid sequence with the HSV-1 TKsequence. For example, Balasubramaniam et al., J. Gen. Virol.71:2979-2987 (1990), provide such an alignment of the following TKenzymes: HSV-1, HSV-2, marmoset herpesvirus, varicella-zoster virus,feline herpesvirus, pseudorabies virus, equine herpesvirus type 1,bovine herpesvirus type 1, turkey herpesvirus, Marek's disease virus,herpesvirus saimiri, and Epstein-Barr virus.

Alternatively, photoaffinity labeling can be used to identify analogousQ substrate binding domains, using the methods described by Rechtin etal., Anal. Biochem. 237:135-140 (1996), which is incorporated byreference. In addition, the identification of a Q substrate bindingdomain can be verified by crystal structure analysis using standardtechniques (see, for example, Wild et al., FEBS Lett. 368:289292, 1995;Brown et al., Nature Struct. Biol. 2:876-881, 1995; De Winter andHerdewijn, J. Med. Chem. 39:4727-4737, 1996). In sum, well-known methodscan be used to identify analogous Q substrate binding domains in variousthymidine kinases. Preferred sources for mutation of the Q substratebinding domain are Herpesviridae thymidine kinases.

The present invention also provides TK mutants that have mutations inthe Q substrate binding domain (or, in the expanded Q substrate bindingdomain) in addition to at least one mutation associated with the DRHnucleoside binding site, as described above. For example, the presentinvention contemplates TK mutants having at least one amino acidsubstitution in the Q substrate binding domain (or, in the expanded Qsubstrate binding domain) and (1) at least two amino acid substitutionslocated toward the N-terminus from a DRH nucleoside binding site (e.g.,one, two or three amino acids toward the N-terminus) and at least onemutation located toward the C-terminus from a DRH nucleoside bindingsite (e.g., four or five amino acids toward the C-terminus), (2) one ormore amino acid substitutions located from one to seven amino acidstoward the N-terminus from a DRH nucleoside binding site, (3) amino acidsubstitutions that are located two to six positions toward N-terminusfrom the DRH nucleoside binding site, and (4) one or more amino acidsubstitutions within the DRH nucleoside binding site. Again, such TKmutants are characterized by an increased biological activity ofthymidine kinase, as compared with unmutated thymidine kinase.

Any of the above-described thymidine kinase mutants may be readilyscreened for increased biological activity, given the assays describedherein and below in the Examples.

Construction of Thymidine Kinase Mutants

Thymidine kinase mutants of the present invention may be constructedusing a wide variety of techniques. For example, mutations may beintroduced at particular loci by synthesizing oligonucleotidescontaining a mutant sequence, flanked by restriction sites enablingligation to fragments of the native sequence. Following ligation, theresulting reconstructed sequence encodes a derivative having the desiredamino acid insertion, substitution, or deletion.

Alternatively, oligonucleotide-directed site-specific (or segmentspecific) mutagenesis procedures may be employed to provide an alteredgene having particular codons altered according to the substitution,deletion, or insertion required. Deletion or truncation derivatives ofthymidine kinase mutants may also be constructed by utilizing convenientrestriction endonuclease sites adjacent to the desired deletion.Subsequent to restriction, overhangs may be filled in, and the DNAreligated. Exemplary methods of making the alterations set forth aboveare disclosed by Sambrook et al. (Molecular cloning: A LaboratoryManual, 2d Ed., Cold Spring Harbor Laboratory Press, 1989).

Thymidine kinase mutants may also be constructed utilizing techniques ofPCR mutagenesis, chemical mutagenesis (Drinkwater and Klinedinst, PNAS83:3402-3406, 1986), by forced nucleotide misincorporation (e.g., Liaoand Wise Gene 88:107-111, 1990), or by use of randomly mutagenizedoligonucleotides (Horwitz et al., Genome 3:112-117, 1989). Preferredmethods for constructing thymidine kinase mutants are set forth in moredetail below in the Examples.

HSVTK Vectors

Within the context of the present invention, the term “thymidine kinasemutant” should be understood to include not only the specific proteindescribed herein (as well as the nucleic acid sequences which encodethese proteins), but derivatives thereof which may include variousstructural fowls of the primary protein which retain biologicalactivity. For example, a thymidine kinase mutant may be in the form ofacidic or basic salts, or in neutral form. In addition, individual aminoacid residues may be modified by oxidation or reduction. Furthermore,various substitutions, deletions, or additions may be made to the aminoacid or nucleic acid sequences, the net effect of which is to retain orfurther enhance the increased biological activity of the mutant. Due tocode degeneracy, for example, there may be considerable variation innucleotide sequences encoding the same amino acid sequence.

Other derivatives of the thymidine kinase mutants disclosed hereininclude conjugates of thymidine kinase mutants along with other proteinsor polypeptides. This may be accomplished, for example, by the synthesisof N-terminal or C-terminal fusion proteins which may be added tofacilitate purification or identification of thymidine kinase mutants(see U.S. Pat. No. 4,851,341, see also, Hopp et al., Bio/Technology6:1204, 1988.)

Within one embodiment of the present invention, truncated derivatives ofthymidine kinase mutants are provided. For example, site-directedmutagenesis may be readily performed in order to delete the N-terminal45 amino acids of a thymidine kinase mutant, thereby constructing atruncated form of the mutant which retains its biological activity.

Mutations in nucleotide sequences constructed for expression ofderivatives of thymidine kinase mutants should preserve the readingframe phase of the coding sequences. Furthermore, the mutations willpreferably not create complementary regions that could hybridize toproduce secondary mRNA structures, such as loops or hairpins, whichwould adversely affect translation of the receptor mRNA. Suchderivatives may be readily constructed using a wide variety oftechniques, including those discussed above.

As noted above, the present invention provides recombinant vectors whichinclude either synthetic, or cDNA-derived nucleic acid moleculesencoding thymidine kinase mutants or derivatives thereof, which areoperably linked to suitable transcriptional or translational regulatoryelements. Suitable regulatory elements may be derived from a variety ofsources, including bacterial, fungal, viral, mammalian, insect, or plantgenes. Selection of appropriate regulatory elements is dependent on thehost cell chosen, and may be readily accomplished by one of ordinaryskill in the art. Examples of regulatory elements include: atranscriptional promoter and enhancer or RNA polymerase bindingsequence, a ribosomal binding sequence, including a translationinitiation signal.

Nucleic acid molecules which encode any of the thymidine kinase mutantsdescribed above may be readily expressed by a wide variety ofprokaryotic and eukaryotic host cells, including bacterial, mammalian,yeast or other fungi, viral, insect, or plant cells. Methods fortransforming or transfecting such cells to express foreign DNA are wellknown in the art (see, e.g., Itakura et al., U.S. Pat. No. 4,704,362;Hinnen et al., PNAS USA 75:1929-1933, 1978; Murray et al., U.S. Pat. No.4,801,542; Upshall et al., U.S. Pat. No. 4,935,349; Hagen et al., U.S.Pat. No. 4,784,950; Axel et al., U.S. Pat. No. 4,399,216; Goeddel etal., U.S. Pat. No. 4,766,075; and Sambrook et al. Molecular Cloning: ALaboratory Manual, 2nd edition, Cold Spring Harbor Laboratory Press,1989; for plant cells see Czako and Marton, Plant Physiol.104:1067-1071, 1994; and Paszkowski et al., Biotech. 24:387392, 1992).

Bacterial host cells suitable for carrying out the present inventioninclude E. coli, B. subtilis, Salmonella typhimurium, and variousspecies within the genus' Pseudomonas, Streptomyces, and Staphylococcus,as well as many other bacterial species well known to one of ordinaryskill in the art. Representative examples of bacterial host cellsinclude DH5α (Stratagene, LaJolla, Calif.).

Bacterial expression vectors preferably comprise a promoter whichfunctions in the host cell, one or more selectable phenotypic markers,and a bacterial origin of replication. Representative promoters includethe β-lactamase (penicillinase) and lactose promoter system (see Changet al., Nature 275:615, 1978), the T7 RNA polymerase promoter (Studieret al., Meth. Enzymol. 185:60-89, 1990), the lambda promoter (Elvin etal., Gene 87:123-126, 1990), the trp promoter (Nichols and Yanofsky,Meth. in Enzymology 101:155, 1983) and the tac promoter (Russell et al.,Gene 20: 231, 1982). Representative selectable markers include variousantibiotic resistance markers such as the kanamycin or ampicillinresistance genes. Many plasmids suitable for transforming host cells arewell known in the art, including among others, pBR322 (see Bolivar etal., Gene 2:95, 1977), the pUC plasmids pUC18, pUC19, pUC118, pUC119(see Messing, Meth. in Enzymology 101:20-77, 1983 and Vieira andMessing, Gene 19:259-268, 1982), and pNH8A, pNH16a, pNH18a, andBluescript M13 (Stratagene, La Jolla, Calif.).

Yeast and fungi host cells suitable for carrying out the presentinvention include, among others Saccharomyces pombe, Saccharomycescerevisiae, the genera Pichia or Kluyveromyces and various species ofthe genus Aspergillus. Suitable expression vectors for yeast and fungiinclude, among others, YC_(p)50 (ATCC No. 37419) for yeast, and the amdScloning vector pV3 (Turnbull, Bio/Technology 7:169, 1989). Protocols forthe transformation of yeast are also well known to those of ordinaryskill in the art. For example, transformation may be readilyaccomplished either by preparation of spheroplasts of yeast with DNA(see Hinnen et al., PNAS USA 75:1929, 1978) or by treatment withalkaline salts such as LiCl (see Itoh et al., J. Bacteriology 153:163,1983). Transformation of fungi may also be carried out usingpolyethylene glycol as described by Cullen et al. (Bio/Technology 5:369,1987).

Mammalian cells suitable for carrying out the present invention include,among others: COS (e.g., ATCC No. CRL 1650 or 1651), BHK (e.g., ATCC No.CRL 6281), CHO (ATCC No. CCL 61), HeLa (e.g., ATCC No. CCL 2), 293 (ATCCNo. 1573) and NS-1 cells. Suitable expression vectors for directingexpression in mammalian cells generally include a promoter, as well asother transcriptional and translational control sequences. Commonpromoters include SV40, MMTV, metallothionein-1, adenovirus E1a,Cytomegalovirus Immediate Early Promoter, and the CytomegalovirusImmediate Late Promoter.

Protocols for the transfection of mammalian cells are well known tothose of ordinary skill in the art. Representative methods includecalcium phosphate mediated transfection, electroporation, lipofection,retroviral, adenoviral and protoplast fusion-mediated transfection (seeSambrook et al., supra).

Thymidine kinase mutants may be prepared by culturing the host/vectorsystems described above, in order to express the recombinant thymidinekinase mutants. Recombinantly produced thymidine kinase mutants may befurther purified as described in more detail below.

As noted above, the present invention also provides a variety of bothviral and non-viral vectors which are suitable for directing theexpression of the nucleic acid molecules described above. Within oneaspect of the invention, viral vectors are provided which comprise apromoter that directs the expression of an isolated nucleic acidmolecule which encodes a thymidine kinase mutant as described above. Awide variety of promoters may be utilized within the context of thepresent invention, including for example, promoters such as MoMLV LTR,RSV LTR, Friend MuLV LTR, Adenoviral promoter (Ohno et al., Science 265:781-784, 1994), Neomycin phosphotransferase promoter/enhancer, lateparvovirus promoter (Koering et al., Hum. Gene Therap. 5:457-463, 1994),Herpes TK promoter, SV40 promoter, Metallothionein IIa geneenhancer/promoter, Cytomegalovirus Immediate Early Promoter, and theCytomegalovirus Immediate Late Promoter. Within particularly preferredembodiments of the invention, the promoter is a tissue-specific promoter(see e.g., WO 91/02805; EP 0,415,731; and WO 90/07936). Representativeexamples of suitable tissue specific promoters include the tyrosinaserelated promoters (TRP-1 and TRP-2, Vile and Hart, Canc. Res.53:962-967, 1993), DF3 enhancer (for breast cells, see Manome et al.,Canc. Res. 54:5408-5413, 1994), SLPI promoter (secretory leucoproteaseinhibitor—expressed in many types of carcinomas, see Garver et al, GeneTherapy 1:46-50, 1994), TRS (tissue specific regulatory sequences, seeDynan and Tjian, Nature 316: 774-778, 1985), albumin and α fetoproteinpromoters (specific for normal hepatocytes and transformed hepatocytes,respectively), the carcino-embryonic antigen promoter (for use intransformed cells of the gastrointestinal tract, lung, breast and othertissues), the tyrosine hydroxylase promoter (for melanocytes), cholineacetyl transferase or neuron specific enolase promoters for use inneuroblastomas, the regulatory sequence for glial fibroblastomas, thetyrosine hydroxylase promoter, c-erb B-2 promoter, PGK promoter, PEPCKpromoter, whey acidic promoter (breast tissue), and casein promoter(breast tissue) and the adipocyte P2 promoter (Ross et al., Genes & Dev.1318-1324, 1993; and Lowell et al., Nature 366:740-742, 1993). Inaddition to the above-noted promoters, other viral-specific promoters(e.g., retroviral promoters (including those noted above, as well asothers such as HIV promoters), hepatitis, herpes (e.g., EBV), andbacterial, fungal or parasitic (e.g., malarial)-specific promoters maybe utilized in order to target a specific cell or tissue which isinfected with a virus, bacteria, fungus or parasite.

Thymidine kinase mutants of the present invention may be expressed froma variety of viral vectors, including for example, adenoviral vectors(e.g., Kass-Eisler et al., PNAS 90(24):11498-502, 1993; Kolls et al.,PNAS 91(1):215-219, 1994; Li et al., Hum Gene Ther. 4(4):403-409, 1993;Vincent et al., Nat. Genet. 5(2):130-134, 1993; and Zabner et al., Cell75(2):207-216, 1993; WO 94/26914, WO 93/9191), adenovirus-associatedviral vectors (Flotte et al., PNAS 90(22):10613-10617, 1993),alphaviruses such as Semliki Forest Virus and Sindbis Virus (Hertz andHuang, J. Vir. 66(2):857-864, 1992; Raju and Huang, J. Vir.65(5):2501-2510, 1991; Xiong et al., Science 243:1188, 1989; U.S. Pat.No. 5,091,309; WO 92/10578; WO 95/07994); baculovirus vectors; herpesviral vectors (e.g., U.S. Pat. Nos. 4,769,331, 4,859,587, 5,288,641 and5,328,688; and PCT publication Nos. WO 94/14971 and WO 95/04139),parvovirus vectors (Koering et al., Hum. Gene Therap. 5:457-463, 1994),pox virus vectors (Ozaki et al., Biochem. Biophys. Res. Comm.193(2):653-660, 1993; and Panicali and Paoletti, PNAS 79:4927-4931,1982), pox viruses, such as canary pox virus or vaccinia virus(Fisher-Hoch et al., PNAS 86:317-321, 1989; Flexner et al., Ann. N.Y.Acad. Sci. 569:86-103, 1989; U.S. Pat. Nos. 4,603,112, 4,769,330 and5,017,487; WO 89/01973); and retroviruses (e.g., Baba et al., J.Neurosurg 79:729-735, 1993; Ram et al., Cancer Res. 53:83-88, 1993;Takamiya et al., J. Neurosci. Res 33:493-503, 1992; Vile and Hart,Cancer Res. 53:962-967, 1993; Vile and Hart, Cancer Res. 53:3860-3864,1993; U.S. Pat. No. 5,219,740; EP 0,415,731; WO 90/07936; WO 91/0285, WO94/03622; WO 93/25698; WO 93/25234; WO 93/11230; WO 93/10218). Withinvarious embodiments, either the viral vector itself, or a viral particlewhich contains the viral vector may be utilized in the methods andcompositions described below.

In addition to viral vectors, non-viral vectors systems, or systemswhich contain portions of a viral vector (e.g., which controltranscription, translation, or viral entry into a cell) may be utilizedto deliver nucleic acid sequences of the present invention.Representative example of such systems a variety of nucleic acid basedtranscription systems (e.g., based on T7 or SP6 promoters, seegenerally, Li et al., “Tumor regression in Nude Mice by Direct Injectionof a Nonviral Cytoplasmic Gene Expression Vector Containing a ThymidineKinase Gene” p. 179, Cold Spring Harbor Meeting in Gene Therapy, Sep.21-25 1194; WO 95/07994). Such vector systems may be administered andprepared as described herein (e.g., in liposomes, condensed withpolycations, or linked to a ligand).

Vectors of the present invention may contain or express a wide varietyof additional nucleic acid molecules in addition to a thymidine kinasenucleic acid molecule as described above. For example, the viral vectormay express a lymphokine, antisense sequence, toxin or “replacement”protein (e.g., adenosine deaminase). Representative examples oflymphokines include IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8,IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, GM-CSF, G-CSF, M-CSF,alpha-interferon, beta-interferon, gamma interferon, and tumor necrosisfactors. Representative examples of antisense sequences includeantisense myc, antisense p53, antisense ras, as well as antisensesequences which block the expression or production of viruses such asHIV, HBV and HCV. Representative examples of toxins include: ricin,abrin, diphtheria toxin, cholera toxin, gelonin, pokeweed antiviralprotein, tritin, Shigella toxin, and Pseudomonas exotoxin A.

Within preferred embodiments of the invention, one or more genes whichencode proteins that facilitate or increase the biological activity ofthymidine kinase may be included with, and expressed by the vectorsdescribed herein. For example, within one embodiment of the invention,nucleic acid molecules which encode DNA polymerase (e.g., a Herpes DNApolymerase) and/or guanylate kinase (Konrad, J. Biol. Chem.267(36):25652-25655, 1992; Miller and Miller, J. Biol. Chem.255(15):7204-7207, 1980) are expressed either from one or severalseparate promoters (e.g., from multiple internal ribosome binding sites)in addition to a thymidine kinase enzyme (either wild type, or thymidinekinase mutants as described above). Representative examples of suchembodiments are set forth in more detail below in Examples 7 and 11. Itshould be understood that although certain nucleic acid molecules aredisclosed which encode DNA polymerase or guanylate kinase, that thepresent invention is not so limited. Indeed, as discussed above withrespect to thymidine kinase mutants, a wide variety of nucleic acidmolecules are considered to be included within the scope of the presentinvention which encode DNA polymerase or guanylate kinase activity(e.g., truncated nucleic acid molecules or nucleic acid molecules whichare degenerate with respect to the encoded amino acid sequence).

Thymidine kinase mutants may also be expressed in non-human transgenicanimals such as mice, rats, rabbits, sheep, dogs and pigs (see Hammer etal. (Nature 315:680-683, 1985), Palmiter et al. (Science 222:809-814,1983), Brinster et al. (Proc. Natl. Acad. Sci. USA 82:4438-4442, 1985),Palmiter and Brinster (Cell 41:343-345, 1985) and U.S. Pat. No.4,736,866). Briefly, an expression unit, including a nucleic acidmolecule to be expressed together with appropriately positionedexpression control sequences, is introduced into pronuclei of fertilizedeggs, for example, by microinjection. Integration of the injected DNA isdetected by blot analysis of DNA from tissue samples. It is preferredthat the introduced DNA be incorporated into the germ line of the animalso that it is passed on to the animal's progeny. Tissue-specificexpression may be achieved through the use of a tissue-specificpromoter, or through the use of an inducible promoter, such as themetallothionein gene promoter (Palmiter et al., 1983, ibid), whichallows regulated expression of the transgene.

Host Cells

The above described nucleic acid molecules which encode thymidine kinasemutants of the present invention (or the vectors which contain and/orexpress these mutants) may readily be introduced into a wide variety ofhost cells. Representative examples of such host cells include plantcells, eukaryotic cells, and prokaryotic cells. Within preferredembodiments, the nucleic acid molecules are introduced into cells from avertebrate or warm-blooded animal, such as a human, macaque, dog, cow,horse, pig, sheep, rat, hamster, mouse or fish cell, or any hybridthereof.

The nucleic acid molecules (or vectors) may be introduced into hostcells by a wide variety of mechanisms, including for example calciumphosphate-mediated transfection (Wigler et al., Cell 14:725, 1978),lipofection; gene gun (Corsaro and Pearson, Somatic Cell Gen. 7:603,1981; Graham and Van der Eb, Virology 52:456, 1973), electroporation(Neumann et al., EMBO J. 1:841-845, 1982), retroviral, adenoviral,protoplast fusion-mediated transfection or DEAE-dextran mediatedtransfection (Ausubel et al., (eds.), Current Protocols in MolecularBiology, John Wiley and Sons, Inc., NY, N.Y., 1987).

Construction of Guanylate Kinase-Thymidine Kinase Fusion Proteins

There are several approaches for improving the net efficiency of suicidegene therapy. As described above, one approach is to create novel TKenzymes that efficiently convert systemically delivered prodrugs intocytotoxic compounds. Another strategy is to facilitate the subsequentmetabolism of the prodrug to its toxic form by introducing the geneencoding the enzyme responsible for the second step in the nucleotidemetabolic pathway of prodrug activation, guanylate kinase, incombination with thymidine kinase. Unlike the cellular thymidine kinase,the HSV TK can perform the initial phosphorylation of produgs, such asGCV and ACV, to their monophosphorylated states. Cellular kinasesfurther phosphorylate the nucleotide to the triphosphate which theninhibits chain elongation by DNA polymerase after insertion into thenascent DNA chain and subsequently leads to cell death. Guanylate kinase(gmk), the second step in the prodrug activation pathway, appears to berate limiting in vivo. Example 11 illustrates methods for theconstruction of mammalian expression vectors that produce both gmk andTK enzymes.

In yet another approach, fusion proteins can be constructed that expressboth gmk and TK enzyme activities, providing the expression of twoenzyme functions from a single promoter and a single cistron. In thisway, the use of a fusion protein for gene therapy would eliminate therequirement for two promoters, and would eliminate the associatedreduction in prodrug activation due to the differences in promoterstrength. Moreover, fusion proteins are advantageous for gene therapyvectors which cannot tolerate large pieces of foreign DNA, such as AAVvectors.

Example 12 describes the construction of two gmk-TK fusion proteins.Although the exemplified vectors contain a TK gene fused to the 3′-endof a gmk gene, suitable fusion proteins can be produced with vectorshaving a gmk gene fused to the 3′-end of a TK gene. Example 12 alsoillustrates that such fusion proteins need not contain the entire aminoacid sequence of a kinase gene. That is, nucleic acid molecules encodinga truncated gmk and/or a truncated TK can be used to express fusionproteins of the present invention. However, such truncated kinases mustpossess the appropriate biological activity, as defined above. Thebiological activity of a truncated gmk or a truncated TK can bedetermined using the enzyme assays described herein.

General methods for producing fusion proteins are well-known to those ofskill in the art. See, for example, Ausubel et al. (eds.), ShortProtocols in Molecular Biology, 3d Edition, pages 16-16 to 16-37 (JohnWiley & Sons, Inc. 1995). Example 11 describes methods for obtainingboth human and murine gmk clones (also see Brady et al., J. Biol. Chem.271:16734-16740, 1996). Those of skill in the art can obtain nucleicacid molecules encoding gmk from a variety of sources using standardtechniques. For example, Konrad, J. Biol. Chem. 267:25652-25655 (1992),describes the isolation of gmk sequences from Saccharomyces cerevisiae,Gaidarov et al., FEBS Lett. 335:81-84 (1993), disclose bovine guanylatekinase sequences, Zschocke et al. Eur. J. Biochem. 213:263-269 (1993),provide porcine guanylate kinase sequences, and an E. coli guanylatekinase sequence is provided by Gentry et al., J. Biol. Chem.268:14316-14321 (1993). In addition, nucleic acid molecules encodingguanylate kinase enzymes are commercially available. For example, DNAmolecules encoding Mycoplasma genitalium gmk can be obtained from theAmerican Type Culture Collection (ATCC No. 623592). Suitable TK genesinclude both known TK genes and the TK mutants of the present invention.Sources for TK genes, suitable expression vectors, and suitable hostcells are described above.

Preparation of Antibodies

Antibodies to the thymidine kinase mutants, guanylate kinase protein, orfusion proteins described herein may readily be prepared given thedisclosure provided herein. Within the context of the present invention,antibodies are understood to include monoclonal antibodies, polyclonalantibodies, antibody fragments (e.g., Fab, and F(ab′)₂) as well asportions thereof that may be produced by various recombinant methods.Antibodies are understood to be reactive against a thymidine kinasemutant or fusion protein if it binds with a K_(a) of greater than orequal to 10⁷ M. As will be appreciated by one of ordinary skill in theart, antibodies may be developed which not only bind to a ligand such asa thymidine kinase mutant or fusion protein, but which also block orinhibit the biological activity of the mutant or fusion protein.

Briefly, polyclonal antibodies may be readily generated by one ofordinary skill in the art from a variety of warm-blooded animals such ashorses, cows, various fowl, rabbits, mice, or rats. Briefly, a thymidinekinase mutant (or guanylate kinase enzyme, or fusion protein, if suchantibodies are desired) is utilized to immunize the animal throughintraperitoneal, intramuscular, intraocular, or subcutaneous injections,an adjuvant such as Freund's complete or incomplete adjuvant. Followingseveral booster immunizations, samples of serum are collected and testedfor reactivity to the thymidine kinase mutant (or guanylate kinase orfusion protein). Particularly preferred polyclonal antisera will give asignal on one of these assays that is at least three times greater thanbackground. Once the titer of the animal has reached a plateau in termsof its reactivity to the thymidine kinase mutant, guanylate kinaseenzyme, or fusion protein, larger quantities of antisera may be readilyobtained either by weekly bleedings, or by exsanguinating the animal.

Monoclonal antibodies may also be readily generated using conventionaltechniques (see U.S. Pat. Nos. RE 32,011, 4,902,614, 4,543,439, and4,411,993 which are incorporated herein by reference; see alsoMonoclonal Antibodies, Hybridomas: A New Dimension in BiologicalAnalyses, Plenum Press, Kennett, McKeam, and Bechtol (eds.), 1980, andAntibodies: A Laboratory Manual, Harlow and Lane (eds.), Cold SpringHarbor Laboratory Press, 1988, which are also incorporated herein byreference).

Briefly, within one embodiment a subject animal such as a rat or mouseis injected with a thymidine kinase mutant, guanylate kinase enzyme, orfusion protein as described above. The thymidine kinase mutant,guanylate kinase enzyme, or fusion protein may be admixed with anadjuvant such as Freund's complete or incomplete adjuvant in order toincrease the resultant immune response. Between one and three weeksafter the initial immunization the animal may be reimmunized withanother booster immunization, and tested for reactivity to the thymidinekinase mutant, guanylate kinase enzyme, or fusion protein using assaysdescribed above. Once the animal has plateaued in its reactivity to themutant, it is sacrificed, and organs which contain large numbers of Bcells such as the spleen and lymph nodes are harvested.

Cells which are obtained from the immunized animal may be immortalizedby transfection with a virus such as the Epstein-Barr virus (EBV) (seeGlasky and Reading, Hybridoma 8(4):377-389, 1989). Alternatively, withina preferred embodiment, the harvested spleen and/or lymph node cellsuspensions are fused with a suitable myeloma cell in order to create a“hybridoma” which secretes monoclonal antibody. Suitable myeloma linesinclude, for example, NS-1 (ATCC No. TIB 18), and P3X63-Ag 8.653 (ATCCNo. CRL 1580).

Following the fusion, the cells may be placed into culture platescontaining a suitable medium, such as RPMI 1640, or DMEM (Dulbecco'sModified Eagles Medium) (JRH Biosciences, Lenexa, Kans.), as well asadditional ingredients, such as Fetal Bovine Serum (FBS, i.e., fromHyclone, Logan, Utah, or JRH Biosciences). Additionally, the mediumshould contain a reagent which selectively allows for the growth offused spleen and myeloma cells such as HAT (hypoxanthine, aminopterin,and thymidine) (Sigma Chemical Co., St. Louis, Mo.). After about sevendays, the resulting fused cells or hybridomas may be screened in orderto determine the presence of antibodies which are reactive against athymidine kinase mutant, guanylate kinase enzyme, or fusion protein. Awide variety of assays may be utilized to determine the presence ofantibodies which are reactive against the proteins of the presentinvention, including for example Countercurrent Immuno-Electrophoresis,Radioimmunoassays, Radioimmunoprecipitations, Enzyme-LinkedImmuno-Sorbent Assays (ELISA), Dot Blot assays, Western Blots,immunoprecipitation, Inhibition or Competition Assays, and sandwichassays (see U.S. Pat. Nos. 4,376,110 and 4,486,530; see also Antibodies:A Laboratory Manual, Harlow and Lane (eds.), Cold Spring HarborLaboratory Press, 1988). Following several clonal dilutions andreassays, a hybridoma producing antibodies reactive against thethymidine kinase mutant (or guanylate kinase enzyme or fusion protein)may be isolated.

Other techniques may also be utilized to construct monoclonal antibodies(see William D. Huse et al., “Generation of a Large CombinationalLibrary of the Immunoglobulin Repertoire in Phage Lambda,” Science246:1275-1281, December 1989; see also L. Sastry et al., “Cloning of theImmunological Repertoire in Escherichia coli for Generation ofMonoclonal Catalytic Antibodies: Construction of a Heavy Chain VariableRegion-Specific cDNA Library,” Proc. Natl. Acad. Sci. USA 86:5728-5732,August 1989; see also Michelle Alting-Mees et al., “Monoclonal AntibodyExpression Libraries: A Rapid Alternative to Hybridomas,” Strategies inMolecular Biology 3:1-9, January 1990; these references describe acommercial system available from Stratacyte, La Jolla, Calif., whichenables the production of antibodies through recombinant techniques).Briefly, mRNA is isolated from a B cell population, and utilized tocreate heavy and light chain immunoglobulin cDNA expression libraries inthe kImmunoZap(H) and klmmunoZap(L) vectors. These vectors may bescreened individually or co-expressed to form Fab fragments orantibodies (see Huse et al., supra; see also Sastry et al., supra).Positive plaques may subsequently be converted to a non-lytic plasmidwhich allows high level expression of monoclonal antibody fragments fromE. coli.

Similarly, portions of antibodies may also be constructed utilizingrecombinant DNA techniques to incorporate the variable regions of a genewhich encodes a specifically binding antibody. Within one embodiment,the genes which encode the variable region from a hybridoma producing amonoclonal antibody of interest are amplified using nucleotide primersfor the variable region. These primers may be synthesized by one ofordinary skill in the art, or may be purchased from commerciallyavailable sources. Stratacyte (La Jolla, Calif.) sells primers for mouseand human variable regions including, among others, primers for V_(Ha),V_(Hb), V_(Hc), V_(Hd), C_(H1), V_(L) and C_(L) regions. These primersmay be utilized to amplify heavy or light chain variable regions, whichmay then be inserted into vectors such as ImmunoZAP™ H or ImmunoZAP™ L(Stratacyte), respectively. These vectors may then be introduced into E.coli for expression. Utilizing these techniques, large amounts of asingle-chain protein containing a fusion of the V_(H) and V_(L) domainsmay be produced (see Bird et al., Science 242:423-426, 1988). Inaddition, such techniques may be utilized to change a “murine” antibodyto a “human” antibody, without altering the binding specificity of theantibody.

Once suitable antibodies have been obtained, they may be isolated orpurified by many techniques well known to those of ordinary skill in theart (see Antibodies: A Laboratory Manual, Harlow and Lane (eds.), ColdSpring Harbor Laboratory Press, 1988). Suitable techniques includepeptide or protein affinity columns, HPLC or RP-HPLC, purification onprotein A or protein G columns, or any combination of these techniques.

Labeling of Antibodies

Anti-thymidine kinase, anti-guanylate kinase, or anti-fusion proteinantibodies which are described above may be labeled with a variety ofmolecules, including for example, fluorescent molecules, toxins, andradionuclides. Representative examples of fluorescent molecules includefluorescein, phycoerythrin, rodamine, Texas red and luciferase.Representative examples of toxins include ricin, abrin diphtheria toxin,cholera toxin, gelonin, pokeweed antiviral protein, tritin, Shigellatoxin, and Pseudomonas exotoxin A. Representative examples ofradionuclides include Cu-64, Ga-67, Ga-68, Zr-89, Ru-97, Tc-99m, Rh-105,Pd-109, In-111, I-123, I-125, I-131, Re-186, Re-188, Au-198, Au-199,Pb-203, At-211, Pb-212 and Bi-212. In addition, the antibodies describedabove may also be labeled or conjugated to one partner of a ligandbinding pair. Representative examples include avidin-biotin, andriboflavin-riboflavin binding protein.

Methods for conjugating or labeling the anti-thymidine kinase,anti-guanylate kinase, or anti-fusion protein antibodies discussed abovewith the representative labels set forth above may be readilyaccomplished by one of ordinary skill in the art (see TrichotheceneAntibody Conjugate, U.S. Pat. No. 4,744,981; Antibody Conjugate, U.S.Pat. No. 5,106,951; Fluorogenic Materials and Labeling Techniques, U.S.Pat. No. 4,018,884; Metal Radionuclide Labeled Proteins for Diagnosisand Therapy, U.S. Pat. No. 4,897,255; and Metal Radionuclide ChelatingCompounds for Improved Chelation Kinetics, U.S. Pat. No. 4,988,496; seealso Inman, Methods In Enzymology, Vol. 34, Affinity Techniques, EnzymePurification: Part B, Jakoby and Wilchek (eds.), Academic Press, NewYork, p. 30, 1974; see also Wilchek and Bayer, “The Avidin-BiotinComplex in Bioanalytical Applications,” Anal. Biochem. 171:1-32, 1988).

Pharmaceutical Compositions

As noted above, the present invention also provides a variety ofpharmaceutical compositions (or medicaments), comprising one of theabove-described thymidine kinase mutants, guanylate kinases, or fusionproteins (e.g. either the nucleic acid molecule, vector, or protein),along with a pharmaceutically or physiologically acceptable carrier,excipients or diluents. Generally, such carriers should be nontoxic torecipients at the dosages and concentrations employed. Ordinarily, thepreparation of such compositions entails combining the therapeutic agentwith buffers, antioxidants such as ascorbic acid, low molecular weight(less than about 10 residues) polypeptides, proteins, amino acids,carbohydrates including glucose, sucrose or dextrins, chelating agentssuch as EDTA, glutathione and other stabilizers and excipients. Neutralbuffered saline or saline mixed with nonspecific serum albumin areexemplary appropriate diluents.

In addition, the pharmaceutical compositions of the present inventionmay be prepared for administration by a variety of different routes,including for example intraarticularly, intracranially, intradermally,intramuscularly, intraocularly, intraperitoneally, intrathecally,intravenously, subcutaneously or even directly into a tumor (forexample, by stereotaxic injection). In addition, pharmaceuticalcompositions of the present invention may be placed within containers,along with packaging material which provides instructions regarding theuse of such pharmaceutical compositions. Generally, such instructionswill include a tangible expression describing the reagent concentration,as well as within certain embodiments, relative amounts of excipientingredients or diluents (e.g., water, saline or PBS) which may benecessary to reconstitute the pharmaceutical composition.

Methods

The present invention also provides methods for inhibiting a pathogenicagent in a warm-blooded animal, comprising administering to thewarm-blood animal a vector (e.g., expression vector, viral vector, orviral particle containing a vector), as described above, such that thepathogenic agent is inhibited. Representative examples of pathogenicagents include autoimmune cells, tumor cells, cells which do not expressor inappropriately express a particular gene, and cells infected withbacteria, viruses, or other intracellular parasites. As will be evidentto one of skill in the art, the amount and frequency of administrationwill depend, of course, on such factors as the nature and severity ofthe indication being treated, the desired response, the condition of thepatient, and so forth. Typically, the compositions may be administeredby a variety of techniques, including for example intraarticularly,intracranially, intradermally, intramuscularly, intraocularly,intraperitoneally, intrathecally, intravenously, subcutaneously or evendirectly into a tumor (for example, by stereotaxic injection).

Within certain embodiments of the invention, the vectors which containor express the nucleic acid molecules which encode thymidine kinase(and/or guanylate kinase) or fusion protein described above, or even thenucleic acid molecules themselves may be administered by a variety ofalternative techniques, including for example administration ofasialoosomucoid (ASOR) conjugated with poly (L-lysine) DNA complexes(Cristano et al., PNAS 92122-92126, 1993), DNA linked to killedadenovirus (Michael et al., J. Biol. Chem. 268(10):6866-6869, 1993; andCuriel et al., Hum. Gene Ther. 3(2):147-154, 1992), cytofectin-mediatedintroduction (DMRIE-DOPE, Vical, Calif.), direct DNA injection (Acsadiet al., Nature 352:815-818, 1991); DNA ligand (Wu et al., J. of Biol.Chem. 264:16985-16987, 1989); lipofection (Feigner et al., Proc. Natl.Acad. Sci. USA 84:7413-7417, 1989); liposomes (Pickering et al., Circ.89(1):13-21, 1994; and Wang et al., PNAS 84:7851-7855, 1987);microprojectile bombardment (Williams et al., PNAS 88:2726-2730, 1991);retrotransposons, transferrin-DNA complexes (Zenke), and direct deliveryof nucleic acids which encode the enzyme itself either alone (Vile andHart, Cancer Res. 53: 3860-3864, 1993), or utilizing PEG-nucleic acidcomplexes.

Within one aspect of the invention, methods are provided for inhibitinga tumor or cancer in a warm-blooded animal, comprising administering tothe warm-blooded animal one of the vectors described above (or nucleicacid molecules which encode thymidine kinase mutants, guanylate kinaseenzymes, or fusion proteins of the present invention), such that thetumor or cancer is inhibited. Within one embodiment, selected cells maybe removed from a warm-blooded animal, one or more of the vectorsdescribed above introduced into the removed cells, and the cellsreintroduced into the same or another warm-blooded animal. Within otherembodiments, vectors or nucleic acid molecules which encode thymidinekinase (or mutants as described herein) or guanylate kinase or fusionprotein may be separately administered or introduced. Within a furtherembodiment, such methods further comprise the step of administering anucleoside analogue. Representative examples of such nucleosideanalogues include ganciclovir, acyclovir, trifluorothymidine,1-[2-deoxy, 2-fluoro, beta-D-arabino furanosyl]-5-iodouracil, ara-A,araT 1-beta-D-arabinofuranoxyl thymine, 5-ethyl-2′-deoxyuridine,5-iodo-5′-amino-2,5′-dideoxyuridine, idoxuridine, AZT, AIU (5-iodo-5′amino 2′,5′-dideoxyuridine), dideoxycytidine and AraC. Briefly,utilizing such methods, a wide variety of tumors (both benign andmalignant) may be treated. Representative examples of such tumorsinclude solid tumors such as lung carcinomas, renal cell carcinomas,breast carcinomas, colorectal carcinomas and melanomas, as well asdiffuse cancers such a leukemias and lymphomas.

Within other aspects of the present invention, methods are provided fortreating a variety of diseases wherein a subset of cells may becharacterized as “diseased” or altered, utilizing the above-describednucleic acid molecules or vectors. Representative examples of suchdiseases include hyperkeratosis (psoriasis), prostate hypertrophy,hyperthyroidism, a wide variety of endocrinopathies, autoimmune diseases(due to autoimmune reactive cells such as certain subsets of T cells),allergies (e.g., by modulating the activity of IgE expressing cellsresponsible for an allergic response), restenosis (e.g., by killingcells which are responsible for the ingrowth and/or clogging of a bloodvessel), a wide array of viral diseases such as AIDS (HIV), hepatitis(HCV or HBV), and intracellular parasitic diseases. Within otherembodiments of the invention, methods are provided for inhibiting thegrowth of or destroying cells which are not traditionally associatedwith a disease. For example, within certain embodiments it may bedesirable to administer a vector (or nucleic acid molecule alone) whichinhibits or destroys fat cells in order to initiate weight loss in ananimal, or to destroy hair follicles (as a depilatory reagent).

Within yet other aspects, vectors which contain or express the nucleicacid molecules encoding thymidine kinase mutants and/or guanylatekinase, or fusion protein (or the nucleic acid molecules themselves) maybe utilized to correct aberrant expression of a gene within a cell, orto replace a specific gene which is defective in proper expression.Representative examples of such diseases include Adenosine DeaminaseDeficiency, Alzheimer's Disease (see, for example, Goat et al., Nature349:704, 1991; Sherrington et al., Nature 375:754, 1995; Levy-Labad etal., Science 269:973, 1995), Cystic Fibrosis, as well as, for example,diseases such as Hemophilia.

Within other aspects of the present invention, methods are provided forutilizing the thymidine kinase mutants or fusion proteins describedabove, as a negative-selection marker gene (see e.g., Czako and Marton,Plant Physiol. 104:1067-1071, 1994) in prokaryotic cells, eukaryoticcells, plants (Czako and Morton, Plant Physiol. 104:1067-1071, 1994),parasites (e.g., Trypanosomes) or viruses. Alternatively, such mutantsmay be utilized as a conditionally lethal marker for homologousrecombination (Mansour et al., Nature 336:348-352, 1988). Arepresentative example is set forth in more detail below as Example 6.

Within other aspects of the present invention, methods are provided fornoninvasive monitoring of gene therapy using thymidine kinase mutantsand fusion proteins having thymidine kinase and guanylate kinaseactivities. Methods have been developed for the noninvasive imaging ofHSV-1 thymidine kinase gene expression using a clinical gamma camera andby single-photon emission tomography with radiolabeled thymidine kinasesubstrate (see, for example, Tjuvajev et al., Cancer Res. 55:6126-6132,1995; Tjuvajev et al., Cancer Res. 56:4087-4095, 1996). The basicapproach is to administer a labeled anti-viral drug that is selectivelyphosphorylated by HSV-1 thymidine kinase and to monitor progress oftherapy using standard scanning methods for human diagnosis. Suitableradiolabeled anti-viral drugs that are substrates for HSV-1 thymidinekinase, such as IVFRU, are well-known to those of skill in the art. See,for example, Wiebe et al., Q. J. Nucl. Med. 41:79-89 (1997), whichcontains a discussion of imaging with radiolabeled nucleoside substratesfor HSV-1 TK that is incorporated by reference. The mutant thymidinekinases and fusion proteins of the present invention that have enhancedthymidine kinase activity provide a means to increase the sensitivity ofsuch noninvasive monitoring.

The following examples are offered by way of illustration, and not byway of limitation.

EXAMPLES Example 1 Construction of TK Mutants Containing Mutations atCodons 165-175 Utilizing a 20% Random Library

Example 1 describes the construction of TK mutants containing mutationsat codons 165 to 175, utilizing a 20% random library. A schematicoutline which depicts the strategy utilized in this example is set forthin FIG. 1.

A. Generation of TK Mutants

1. Generation of Oligonucleotides

A 52-mer oligonucleotide with a wild-type tk sequence (SEQUENCE ID. No.2) and a 56-mer that contained degenerate nucleotides spanning fromcodon 165 through 175 (SEQUENCE ID. No. 3) of the tk gene (FIG. 23discloses nucleotides in the open reading frame of HSVTK-1 [SEQUENCE IDNO. 1]), (where N=80% wild-type nucleotides and a 20% mixture of theother three at each position) were synthesized by Operon Technologies(San Pablo, Calif.). Both oligomers were complementary to each otheralong 12 bases at their 3′-ends.

(SEQUENCE ID No. 2) 5′-TG GGA GCT CAC ATG CCC CGC CCC CGG CCC TCA CCCTCA TCT TCG ATC GCC AT-3′ (SEQUENCE ID No. 3)5′-ATG AGG TAC CGN NNN NNN NNN NNN NNN NNN NNN NNN NNN NNN NNA TGG CGA TCG AA-3′

For the construction of pKTPD described below, two additionaloligonucleotides were synthesized by Operon Technologies usingphosphoramide chemistry. These oligonucleotides were:

5′-CCC CTC GAG CGC GGT AC-3′ (SEQUENCE ID No. 4)5′-CGC GCT CGA GGG GAG CT-3′ (SEQUENCE ID No. 5)

2. Generation of Random Sequence-Containing Libraries

a. Construction of Vectors pMDC and pMCC

Chimeric vectors pMDC (which produces an inactive TK gene product) andpMCC (which produces wild-type TK) were produced from plasmids pHETK1and pHETK2 essentially as described below. Briefly, plasmids pHETK1 andpHETK2 (Waldman et al., J. Biol. Chem. 258:11571-11575, 1983) areexpression vectors that contain a HSV-1 tk structural gene, and arederivatives of pBR322. Restriction maps of pHETK1 and pHETK2 can befound in Waldman et al, J. Biol. Chem. 258:11571-11575, 1983, whichdescribes the construction of these plasmids. Plasmid pHETK2 containsλP_(L) and λP_(R) promoters, ampR, and the c1857 temperature-sensitiverepressor, whereas pHETK1 contains all the above except the λP_(L)promoter. Plasmids pHETK1 and pHETK2 were obtained from Dr. WilliamSummers (School of Medicine, Yale University, New Haven).

In order to construct pMDC and pMCC, a dummy vector, designated pKTPDwas first constructed as described by Dube et al. in Biochem.30:11760-11767, 1991. Briefly, oligonucleotides SEQUENCE ID Nos. 4 and 5(20 pmol of each) were first phosphorylated and then annealed to form adouble-stranded oligonucleotide with KpnI- and SstI-compatible ends andwith an internal XhoI site. In addition, pHETK2 was digested with SstIand KpnI restriction endonucleases, and the large fragment isolated byagarose gel electrophoresis and subsequent electroelution. Two picomolesof the large fragment was ligated with 6 pmol of the double-strandedoligonucleotide. The resultant double-stranded circular DNA product(designated “pKTPD”) was used to transform competent E. coli KY895cells. E. coli KY895 is a TK-deficient strain (K12 tdk⁻, F⁻, ilv 276)obtained from William Summers, Yale University, New Haven, Conn. Clonescontaining the recombinant plasmid pKTPD grow on LB plates containing 50μg/mL carbenicillin. The presence of recombinant plasmid DNA wasverified by the cleavage at the XhoI site. The inability of pKTPD tosupport the growth of E. coli KY895 in the thymidine kinase selectionmedium indicates that it does not produce a functional thymidine kinase.

pHETK1 and pKTPD were then utilized to construct a new chimeric dummyvector, designated pMDC. Briefly, upon digestion with SphI and PvuIIpHETK1 is cut into two fragments. The larger fragment contains ampR,cI857, λP_(R) sequences, and part of the tk gene spanning from the BamHIto the SphI site. The smaller fragment contains the remainder of the tkgene from SphI to PvuII. Similarly, pKTPD upon digestion with the sametwo enzymes is cut into one larger and one smaller fragment. The smallerSphI/PvuII fragment of pKTPD contains a dummy or inactive sequencewithin the KpnI and SacI sites of the tk gene. Ligation of the largerfragment from pHETK1 with the smaller fragment of pKTPD results in achimeric vector, pMDC, that produces an inactive tk gene product.

Another chimeric vector, pMCC, containing the wild-type tk gene wassimilarly constructed by ligating the larger fragment from pHETK1 withthe smaller fragment of pHETK2. As noted above, PMCC produces activewild-type TK.

b. Generation of a Library

A library containing 20% random nucleotide sequences was constructed asfollows. Briefly, a 52-mer oligo containing wild-type sequences(SEQUENCE ID No. 2) was hybridized to a 56-mer oligo which containeddegenerate sequences spanning codons 165 through 175 (Sequence ID No 3).

The hybrid was extended with the Klenow fragment of E. coli DNApolymerase I to produce a complete double-stranded DNA product. Thisstrategy was implemented in order to avoid synthesizing a long randomnucleotide containing SEQUENCE ID No. 3, since the locations of KpnI andSacI sites (insertion sites) in the vector require a long cassette. TheKlenow fragment generated double-stranded DNA was then subjected topolymerase chain reaction amplification by using two synthetic primers:the first primer, a: 5′-TGG GAG CTC ACA TGC CCC GCC-3′ (SEQUENCE ID No.6) corresponds to the 21-base sequence of 5′ terminus of oligo SEQUENCEID No. 2. The second primer, b: 5′-ATG AGG TAC CG-3′ (SEQUENCE ID No. 7)corresponds to the 11-base sequence of 5′ terminus of oligo SEQUENCE IDNo. 3. The polymerase chain reaction amplification reactions contained20 mM Tris-HCl (pH 8.3), 25 mM KCl, 1.5 mM MgCl₂, and 0.05% Tween 20,0.1 mg/ml BSA, 50 μM each of the four deoxynucleoside triphosphates, 20pmol of primer “a,” 40 pmol of primer “b,” approximately 1 pmol of theextended double-stranded oligonucleotide as template, and 2 units of Taqpolymerase (Cetus) in 100-μl final reaction volumes. Each mixture wasoverlaid with mineral oil and subjected to 30 rounds of temperaturecycling: 94° C. for 1 minute, 34° C. for 2 minutes, and 72° C. for 7minutes.

Low molecular weight components and excess primers were removed from thepolymerase chain reaction-amplified product by centrifugation with aCentricon 30 ultrafiltration unit, and the amplified DNA was digestedwith KpnI and SacI. The digested double-stranded oligonucleotidecontaining the random sequence was again purified by a Centricon 30unit, and ligated to the KpnI/SacI digested large fragment of pMDC at10:1 molar ratio in the presence of 1 mM ATP and 1 unit of T4 DNA ligase(BRL) in a volume of 10 μl. Incubation was for 18 hours at 14° C. andthe reaction was terminated by phenol-CHCl₃ extraction followed byethanol precipitation.

c. Selection of TK Mutants

The precipitate described above was dried and dissolved in 10 μl ofwater, and used to transform competent E. coli KY895 by electroporation.One μl of ligated product was mixed with 50 μl of competent cells andelectroporated at 2 KV, 25 μF, and 400 Ohms with a Gene-pulserelectroporator (Bio-Rad). After the pulse, 1 ml of SOC medium (2%Bactotryptone, 0.5% Bacto yeast extract, 10 mM NaCl, 2.5 mM KCl, 10 mMMgCl₂, 10 mM MgSO₄ and 20 mM glucose) was added, followed by incubationat 37° C. for 1.5 hours with continuous agitation. An aliquot of eachtransformation solution was spread onto LB-agar medium containing 50μg/ml of carbenicillin to determine total number of transformants.Selection for active TK clones was performed on TK selection medium thatcontained 50 μg/ml of carbenicillin. 10 μg/ml of 5′ fluorodeoxyuridine,2 μg/ml of thymidine, 20 μg/ml of uridine. 2% BBL peptone, 0.5% NaCl,0.2% glucose, and 0.8% Gel-Rite (Scott Laboratories, Inc., Carson,Calif.) (FIG. 1). Colonies on carbenicillin medium were incubated at 37°C. for 14-16 hours, whereas inoculated TK selection medium was incubatedat 37° C. for 24 hours.

From a total of 53,000 transformants that grew on carbenicillin medium,190 were able to complement E. coli KY 895 for TK function.

Example 2 Construction of TK Mutants Containing Mutations at Codons165-175 Utilizing a 100% Random Library

Example 2 describes the construction of TK mutants containing mutationsat codons 165-175 utilizing a 100% random library. The strategy whichwas utilized for this example is similar to that described in Example 1above.

A. Generation of TK Mutants

Generation of Oligonucleotides

A 52-mer 5′-d(TG GGA GCT CAC ATG CCC CGC CCC CGG CCC TCA CCC TCA TCT TCGATC GCC AT)-3′ (SEQUENCE ID No. 8) with a wild-type tk sequence and KpnI site at the 5′ end was synthesized by Operon Technologies (San Pablo,Calif.). In addition, a 56-mer containing random nucleotidescorresponding to HSV-1 tk codons 165-175 and containing a Sac I site atthe 3′ end 5′ -d(ATG AGG TAC CGN NNN NNN NNN NNN NNN NNN NNN NNN NNN NNNNNA TGG CGA TCG AA)-3′ (SEQUENCE ID No. 3), where N=equimolarconcentrations of G, A, T, or C, was also synthesized. Theoligonucleotides were separated by electrophoresis through a 20%denaturing polyacrylamide gel, followed by purification on areverse-phase mini column (Glen Research, Sterling, Va.).

2. Generation of a 100% Random Sequence—Containing Library

The 52-mer corresponding to the wild-type HSV-1 tk sequence washybridized with the 56-mer containing random nucleotides. The hybrid wasthen extended with the Klenow fragment of DNA polymerase I, PCRamplified, and ligated into pMDC essentially as described above inExample 1.

3. Selection of TK⁺ Mutants

Functional TK mutants were identified by colony formation onTK-selection medium based on their ability to phosphorylate dTessentially as described below. Briefly, the ligated product wasintroduced into tk⁻ E. coli strain KY895. The total number oftransformants was determined by plating on LB agar containing 50 μg ofcarbenicillin per mL and the number of transformants that producedcatalytically active thymidine kinase was determined by plating onTK-selection medium [2% BBL peptone, 0.5% NaCl, 0.2% glucose, 0.8%Gel-Rite (Scott Laboratories, Carson, Calif.)], 50 μg 1 mL ofcarbenicillin, 10 μg/mL of fluorodeoxyuridine, 2 μg/mL of dT, and 20μg/mL of uridine.

Two million (2×10⁶) transformants were screened from the 100% randomlibrary, of which 1540 formed colonies on the TK-selection medium.

B. Selection of AZT-Sensitive Mutants

A subset of 690 mutants from the 100% random library (TKI) and 190mutants from the 20% degenerate library (TKF) (described above inExample 1) were subjected to secondary negative selection on mediumcontaining AZT in order to identify mutants that exhibited enhancedphosphorylation of AZT. This screen is based upon the premise thatmutants with increased ability to phosphorylate AZT relative to dT wouldbe unable to form colonies on the AZT-selection medium. In particular,the product, AZT monophosphate would be further phosphorylated by thehost cell's nonspecific nucleotide kinases, or possibly by the mutantTK, incorporated into bacterial DNA by host DNA polymerases, terminateDNA synthesis, and thus prevent replication of the host chromosome.

Briefly, the TK mutants were first grown as individual colonies onTK-selection medium (1.0 μg/mL of dT), and then replica plated ontoAZT-selection medium (0.05 μg/mL of AZT, 1.0 μg/mL of dT). All othercomponents in the AZT-selection medium were the same as the TK-selectionmedium. Those TK mutants which failed to grow on the AZT-selectionmedium were selected and retested for growth on both TK- andAZT-selection media separately.

Of the 880 primary selectants that were screened, only two mutants, TKF105 (from the 20% library) and TKI 208 (from the 100% library), formedcolonies on the TK-selection medium at an efficiency similar to that ofE. coli harboring the wild-type plasmid but not on the AZT-selectionmedium (FIG. 2).

The nucleotide and deduced amino acid sequences of TKF 105 and TKI 208are presented in FIG. 3. Both mutants contain a single amino acidsubstitution at the same position: Leu-170 was changed to Ile in TKF 105and to Val in TKI 208. No other substitutions were observed in thesurrounding 220 nucleotides.

To ensure that the difference between TKF 105 and TKI 208 was not due todifferential expression of TK in E. coli harboring mutant and wild-typeplasmids, Western blots of extracts from cells containing either TKI 208or wild-type plasmids were compared. No significant difference wasobserved in the amount or electrophoretic mobility of immunoreactivestaining protein. Also, the rate of dT phosphorylation per mg of proteinwas determined, and found to be similar in extracts of E. coli harboringTKI 208, TKF 105, and wild-type plasmids.

In order to show that the lack of growth of these two mutants onAZT-selection medium was due to enhanced phosphorylation of AZT, thefollowing experiments were conducted.

1. Rate of [³H]AZT Uptake

First, the rate of [³H]AZT uptake relative to [³H]dT into E. coliharboring wild-type and mutant plasmids was determined. These studiesindicated that E. coli harboring the AZT-sensitive mutants, TKF 105 andTKI 208, exhibited a 4-fold increase in the ratio of AZT to dT uptake,as compared to E. coli with the wild-type plasmid.

2. Affinity Purification of TK

Purification of wild-type and mutant TKs was performed by affinitychromatography on CH-Sepharose 4B (Pharmacia) coupled top-aminophenylthymidine 3′-phosphate. Briefly, crude bacterial extractwas passed three times through a 7-mL bed-volume affinity column. Thecolumn was then washed sequentially using 30 mL each of buffer A [0.1 MTris HCl, pH 7.5/5 mM dithiothreitol (DTT)/10% glycerol], buffer B (0.1MTris-HCl, pH 7.5/0.5 M KCl/5 mM DTT/10% glycerol), and buffer A. TK waseluted using a 60-mL, linear gradient of 0-600 μM dT in buffer C (0.3 MTris HCl, pH 7.4/50 mM KCl/10% glycerol). Active fractions were pooledand dialyzed against three changes each of 2 liters of 50 mM Tris-HCl,pH 7.4/5 mM DTT/10% glycerol. Except in the final dialysis, all theabove buffers contained 50 μg/mL of aprotinin and 2 μg/mL each ofpepstatin and leupeptin.

3. Kinetics of AZT Phosphorylation

Secondly, the kinetics of AZT phosphorylation by the two mutants wasdetermined. Briefly, reactions were carried out in a final volume of 100μl containing 50 mM Tris-HCl (pH 7.5), 5 mM ATP. 4 mM MgCl₂, 2.5 mM DTT,12 mM KCl, 0.18 mg/mL of bovine serum albumin, 5% glycerol, 0.08 μCi of[³ H]AZT (Sigma), various concentrations of unlabeled AZT (0-4.0 μM),and purified enzymes (4 and 1.2 units, respectively, for wild-type andTKI 208). (One unit of enzyme is defined as that amount that canphosphorylate 1.0 pmol of dT to TMP in 1 minute under the conditionsdescribed above.) Incubation was at 34° C.±1° C. for 10 minutes, andreactions were stopped by adding 1.0 mM unlabeled dT and cooling on ice.Half of the reaction mixtures were pipetted onto a DEAE-cellulose disc(25 mm), dipped in distilled water (1 minute), followed by four washesin absolute ethanol. The amount of radioactivity adsorbed to the discwas determined by scintillation spectroscopy. K_(m) and V_(max) valueswere determined by using the Cleland SUBIN program (Cleland, MethodsEnz. 63:103-138, 1979). The values for k_(cat) were calculated using theequation V_(max)=k_(cat)[E]_(o), where [E]_(o)=total enzymeconcentration. TK assays wherein phosphorylation of dT was measured werecarried out in a final volume of 50 μl using 0.3 μCi ([3H-methyl]dT: 87Ci/mmol: Amersham), various concentrations of unlabeled dT (0-4.0 μM),and 1.1 and 0.5 units of TK for the wild-type and TKI 208, respectively.All other components in the reaction mixtures and the incubationconditions were as described above for phosphorylation of AZT.

As shown below in Table I, the AZT-sensitive variant TKI 208 exhibits alower K_(m) (4.4 μM) compared to that of the wild-type (8.5 μM). Bycomparing the k_(cat)/K_(m) between the two substrates (AZT vs. dT), itcan be seen that TKI 208 selectively phosphorylates AZT 2.3-fold moreefficiently than dT. Similar preliminary experiments with purified TKF105 TK also showed lower K_(m) (3.7 μM) for AZT, but similar values fork_(cat)/K_(m) compared to the wild-type.

TABLE I ABILITY OF WILD-TYPE AND TKI 208 TKS TO PHOSPHORYLATE AZT AND DTPhos- k_(cat)/K_(m) k_(cat)/K_(m) (AZT) phorylation k_(m), μM k_(cat),s⁻¹ s⁻¹, M⁻¹ k_(cat)/K_(m) (dT) AZT Wildtype 8.46 ± 1.3  3.6 × 10⁻²  4.2×. 10³ 1.7 ×. 10⁻³ TKI 208 4.40 ± 0.43* 3.0 × 10⁻²  6.5 × 10³ 4.0 × 10⁻³dT Wildtype 0.475 ± 0.10  1.21  2.5 × 10⁶ TKI 208 0.35 ± 0.008 0.56 1.57× 10⁶ 

C. Thermostability Analysis of Mutant TKs

Mutants were, analyzed for thermostability essentially as describedbelow. Briefly, 25 μg of each extract were preincubated in 0.3 mL of 28mM Tris-HCl, pH 7.5 containing 0.28 mg/mL of bovine serum albumin, 28μg/mL of aprotinin, 2 μg/mL (each) of pepstatin and leupeptin, at 42° C.for 0.5, 10, 20, 30, or 40 minutes. At each time point 30-μl (2.5 μg)aliquots were assayed for residual TK activity in a total reactionvolume of 50 μl containing 50 mM Tris-HCl (pH 7.5), 5 mM ATP, 4 mMMgCl₂, 2.5 mM DTT, 12 mM KCl, 0.18 mg/mL of bovine serum albumin, 5%glycerol, and 1 μM [³H-methyl]dT (60×10³ dpm/pmol). Incubation was at34° C. for 10 minutes. The reaction was stopped by cooling on ice, and25 μl was pipetted onto a DEAE-cellulose disc. Wash and assay conditionsfor the discs were performed as described for the AZT assay above.

Assay results of unfractionated extracts of TKF 2, TKF 56, TKF 75, TKF446 and wild-type TK are shown in FIGS. 4A-4D. One of the mutants, TKF2, was more thermostable at 42° C. than any of the other mutants, orthan the wild-type. Except for TKF 2, all of the mutants tested,including the wild-type, had ratios of residual activity afterpreincubation at 42° C. compared to 34° C. of 0.05-0.30: TKF 2 had aratio of 0.7. TKF 2 contains three amino acid substitutions:Pro-165→His, Ala-167→Ser, and Ala-174→Val (FIG. 3). TKF 75 contained anAla-167→Ser substitution, TKF 56 a Ala-174→Val, and TM 440 a Pro-165→Alasubstitution. The thermolability of mutants TKF 56 and TKF 75 withAla-174→Val and Ala-167→Ser substitutions, respectively, was similar tothat of the wild-type. Both lost >80% of their activity after incubationfor 5 minutes at 42° C. TKF 440 with a Pro-165→Ala is more stable, butnot as stable as TKF 2, the triple mutant.

Two types of experiments were carried out to verify the thermostabilityof TKF 2. First, TK protein from TKF 2 and the wild-type plasmidharboring E. coli were purified to near homogeneity by affinitychromatography, and assayed as described above. As before, loss ofactivity is less in TKF 2 than in the wild-type after preincubation at42° C. (FIG. 4E).

Secondly, tk genes from TKF 2 and wild-type TK were transferred into avector with a promoter for T3 RNA polymerase. More specifically, thefull-length Bgl II-Pvu I fragments of tk genes from wild-type and TKF 2plasmids were isolated and subcloned into the pBluescript SK⁺(Stratagene) vector between the Spe I and EcoRI sites with the use ofsynthetic linkers. In vitro transcription using the T3 promoter wascarried out using the Promega transcription system. In vitro translationwas carried out using a reticulocyte lysate system (Promega) followingthe supplier's protocol. The loss of TK activity of the in vitrosynthesized proteins from the wild-type and TKF 2 tk genes as a functionof preincubation at 42° C. is shown in FIG. 5. The protein encoded byTKF 2 lost <10% of its activity after preincubation for 45 minutes. Incontrast, the protein encoded by the wild-type gene lost >80% of itsinitial activity. The degree of thermostability exhibited by the invitro synthesized TKF 2 was similar to or greater than that of crudeextracts harboring the original TKF 2 plasmid. For SDS/PAGE analysis,the translated products were labeled with [³⁵S]methionine.

An autoradiograph of the labeled proteins after SDS/PAGE is shown inFIG. 6. The arrow indicates the expected size of translated TKs asjudged by molecular mass standards (Bio-Rad). From this autoradiographit is evident that the translation products migrate as double bands, oneof which corresponds to a protein of 43 kDa, which is in accord with thereported size of HSV-1 TK expressed in E. coli. The second band could bedue to the proteolytic degradation of a 32-residue fragment at theamino-terminal end, which does not detectably alter TK activity of theHSV-1 TK.

Example 3 Construction and Analysis of TK Mutants with Mutations atCodons 155, and 161 to 165 Utilizing a 20% Random Library

This example describes the construction and analysis of TK mutants whichare mutagenized at codons 155, and 161 through 165. Bacterial strainsand materials which were utilized within this example are set forthbelow.

Bacterial Strains. E. coli strain KY895 (F⁻, tdk⁻, 1-ilv), originallydescribed by. Igarashi et al. (Genetics 57:643-654, 1967), was used inthe genetic complementation assays for thymidine kinase activity. E.coli strain NM522 (F′ lacI^(q) Δ (lacZ)M15 proAB/supE thi Δ (lacproAB)Δ(hsdMS-mcrB)5(r_(k) ⁻McrB⁻)) (NEB, Beverly, Mass.) was used as arecipient in all subcloning experiments. Helper phage VCM13 (Stratagene,La Jolla, Calif.) was used in the production of single-stranded phagefor sequencing.

Materials. L-[³⁵S]Methionine/cysteine (specific activity, 1140 Ci/mmol)for protein synthesis determination and [methyl-³H] thymidine (specificactivity, 87 Ci/mmol) were purchased from Amersham. Other radioisotopes[[side chain-2-³H] acyclovir (specific activity, 28.6 Ci/mmol) and[5³H]-deoxycytidine (specific activity, 29 Ci/mmol)] were purchased fromDu Pont-New England Nuclear (Boston, Mass.), and [8⁻³H] ganciclovir(specific activity, 22 Ci/mmol) and [methyl⁻³H]-3′-azido-3′deoxythymidine (specific activity, 14 Ci/mmol) were from Moravek (Brea,Calif.). Restriction endonucleases and T4 DNA ligase were purchased fromNew England Biolabs (NEB). Promega (Madison, Wis.) was the source of thein vitro transcription and translation reagents except for the capanalog, (5′)Gppp(5′)G, which was purchased from NEB. Oligonucleotidesused for sequencing and polymerase chain reaction amplifications wereobtained from Operon (Alameda, Calif.). Other chemicals were purchasedfrom Sigma (St. Louis, Mo.) except where designated.

A. Generation of TK Mutants

1. Generation of Oligonucleotides

Two oligonucleotides were synthesized by American Synthesis, Inc.(Pleasanton, Calif.): MB 110 (70 mer) 5′-TGGGAGCTCA CATGCCCCGCCC[CCG]GCCCT CACCCTCATC [TTCGACCGCC ATCCC]ATCGC CGCCCTCCTG-3′ (SEQUENCEID No. 9), and MB111 (38 mer) 5′-ATGAGGTACC GCGCAGCTGG GTAGCACAGGAGGGCGGC-3′ (SEQUENCE ID No. 10). Within these oligonucleotides,nucleotides in brackets where synthesized as 80% wild-type nucleotide,and 20% the other three nucleotides.

At the 5′ end of MB 110 is a SacI restriction site and, at the 5′ end ofMB111, a KpnI site. These restriction sites were utilized at a laterstep after second-strand synthesis occurred. Furthermore, as an internalcontrol, a PvuII site was introduced (silent change) in MB 111 in orderto allow confirmation of random sequence insertion prior to sequencing.Twelve nucleotides at the 3′ ends of each oligonucleotide arecomplementary to allow for hybridization of the two strands to eachother. Each oligonucleotide was subjected to electrophoresis on a 20%acrylamide-urea gel and visualized by UV shadowing on a PEI-celluloseTLC plate (Baker, Phillipsburg, N.J.), the portion of the gel containingthe correct sized oligonucleotide was excised, and the oligonucleotidewas eluted from the gel in 0.5M NH4Ac/10 mM MgOAc₂ overnight at 37° C.The eluted oligonucleotide was then ethanol-precipitated and resuspendedin H2O. An OD₂₆₀ measurement was taken, and the extinction coefficientfor each oligo was used to determine the concentration.

Equimolar amounts of MB 110 and MB 111 (25 pmol) were annealed in asmall volume (20 μl) in 1× annealing buffer (10× annealing buffer=70 mMTris (pH 7.5)/60 mM MgCl₂/200 mM NaCI) for 5 minutes at 95° C., thenmoved to 65° C. for 20 minutes, followed by slow cooling to roomtemperature. To the annealed oligonucleotides (20 μl) were added 2 μl of10× annealing buffer, 2.80 of 10 mM dNTPs, 0.8 μl of 0.1M ofdithiothreitol (DTT), 2.4 μl of DNA polymerase I Klenow fragment (5units/μl), and H₂O to bring the volume to 40 μL. The mixture was placedat 37° C. for 30 minutes, at 65° C. for 10 minutes, and finally at roomtemperature for 10 minutes. Verification of fully extended radioactiveoligonucleotides was accomplished by subjecting the samples todenaturing acrylamide gel electrophoresis and autoradiography.Amplification of the extended products was performed using thepolymerase chain reaction with Taq polymerase (Stratagene). The 100 uLreactions contained 20 mM Tris (pH 8.3)/25 mM KCl/1.5 mM MgCl₂/0.05%Tween 20)/0.1 mg/mL BSA/50 μM of each of the four deoxynucleosidetriphosphates (dNTPs)/22 pmol PCR primer 1/20 pmol PCR primer 2/2 unitsof Taq polymerase and 6 pmol of the extended random oligonucleotide;Primer 1=5′ TGGGAGCTCACATGCCCCGCC-3′ (SEQUENCE ID No. 6) and primer2=5′-ATGAGGTACCG-3′ (SEQUENCE ID No. 7). One drop of mineral oil wasadded to each tube, which was then placed in a Perkins Elmer-Cetusthermal cycler (Norwalk, Conn.) and programmed for 30 cycles of 95° C.for 1 minute and 34° C. for 2 minutes. At the end of the 30 cycles, thereactions were left at 72° C. for 7 minutes, and then the cycler wasmaintained at 4° C. After confirmation of amplification by 2% agarosegel electrophoresis, the product-containing reactions were pooled,precipitated and digested with KpnI and SacI. Doubly restrictedfragments were distinguished from single cut or uncut fragments onnon-denaturing acrylamide gels, and the appropriate fragment was excisedand isolated as described above.

2. Generation of Random Sequence-Containing Libraries

Cesium chloride gradient purified pMDC (“dummy” vector) which wasconstructed as described above in Example 1, digested with KpnI and SacIrestriction endonucleases, and gel-isolated from a 1% agarose/1× TBE gelusing GenClean II (Bio101, La Jolla, Calif.). This vector was ligatedwith the gel-isolated PCR-amplified random fragment overnight at 16° C.with 1 unit of T4 DNA ligase.

3. Selection of TK Mutants

The ligated mixture was then used to transform KY895 by electroporation(BioRad gene pulser, 2 kV, 25 μF, 400Ω). Briefly, cells were preparedfor electroporation according to a protocol provided by BioRad(Richmond, Calif.). After each pulse, 1 mL of SOC (2% Bactotryptone/0.5%yeast extract/10 mM NaCl/2.5 mM KCl/10 mM MgCl₂/10 mM MgSO₄/20 mMglucose) was added to the curette and the electroporation mixturetransferred to a 25 mL snap-cap Falcon tube. After the tubes were shakenfor 1 hour at 37° C., the cells were plated onto LB plates [per liter:10 g tryptone/5 g of yeast extract/10 g NaCl (pH 7)] containingcarbenicillin (50 μg/mL), (“LB+carb⁵⁰ plates”) and incubated at 37° C.overnight. The number of colonies was counted, picked with a toothpick,and streaked on TK selection media [2% BBL Trypticase peptone (BectonDickenson, Cockeysville, Md.)/0.5% NaCl/0.8% Gel-Rite (ScottLaboratories, Carson, Calif.)/0.2% glucose/50 μg/mL carbenicillin/10μg/mL 5′-fluorodeoxyuridine/2 μg/mL thymidine/12.5 μg/mL uridine]. Thebasis of this selection is that 5′-fluorodeoxyuridine (FUdR) isphosphorylated by thymidine kinase to form FdUMP, an inhibitor of the denovo pathway enzyme, thymidylate synthase. The requirement for dTMP canthen be fulfilled only by an active thymidine kinase. Uridine issupplied to inhibit thymidine phosphorylase. After 16-24 hours, the 1Kselection plates were scored for growth, and any positives picked andrestreaked on TK selection plates and LB+carb⁵⁰ plates to confirm thephenotype.

Approximately 260 random transformants were screened for their abilityto complement KY895, a TK-deficient E. coli on TK selection media. Ofthese, 82 were scored as positives and sequenced. Therefore,approximately 32% of all transformants encoded functional enzymes.

B. Analysis of Mutants

TK mutants were isolated and sequenced as follows. Briefly, mutant DNAwas isolated from overnight cultures grown in 2× YT (per liter: 16 gtryptone/10 g of yeast extract/5 g NaCl)+carb⁵⁰ using the Promega Magicminiprep kit according to the manufacturer's instructions, except that 3mLs of culture was used per isolation because of the low copy number ofthe plasmid. Ten microliters of each dsDNA was alkaline-denatured,precipitated, and resuspended in Sequenase reaction buffer, H₂O, andsequencing primer (5′-CATGCCTTATGCCGTGA-3′) (SEQUENCE ID No. 11). Theprimer was then annealed, and the DNA subjected to dideoxy sequencing(Sanger et al., 1977) using Sequenase according to the manufacturersinstructions (USB, Cleveland, Ohio).

Eleven of the clones encoded wild-type amino acid sequence (13.4%), withseven of these containing the wild-type nucleotide sequence. Threeclones with wild-type amino acid residues contained single nucleotidechanges (all different), and one contained three nucleotide changes. Asshown in Table IA below, a total of 49 TK positive clones containingsingle amino acid changes (59.8%) were identified. Nineteen double aminoacid mutations (23.2%), two triple (2.4%) and one clone containing fouramino acid changes (1.2%) were identified. Within Table IA, wild-typeHSV-1 TK amino acids mutated are given in the boldface box with theresidue number and the type of residue found in the majority ofsequences [O=hydrophobic; I=hydrophilic; (+)=positively charged;(−)=negatively charged residues]. Below the wild-type residue are thenumber of times a particular amino acid substitution was found. In thebottom section, the percentages of each type of residue found arelisted.

The amino acid sequences of clones with multiple alterations are shownin Table 1B. The wild-type amino acids and their positions in the HSV-1TK polypeptide are indicated at the top of the table. Double, triple,and quadruple amino acid substitutions are shown in the respectivecategories. If a set of mutations was identified more than once, thenumber of occurrences is noted on the left in parentheses.

TABLE IA Wild-type O O (−)I (+)I (+)I O Sequence P F D R H P 155 161 162163 164 165 Substitutions 3L 4I 5E 5C 3N 3L at Each 2A 4Y 1G 1S 1T 2TPosition 2T 3C 2S 1Q 2L 1N 1R 1S 1A Types of 11% (+) 57% I 83% (−)I 100%I 100% I 10% (+) Substitutions 33% I 43% 0 17% I 50% I 56% O 40% O

TABLE IB Number of P F D R H P changes 155 161 162 163 164 165 Doubles AV Q I Q E R E (4) R G T E (2) I H I R N S Y C N K (2) E N P Q Q L Q E LTriples A P T Quadruple N S N A

C. Secondary Screening and Subcloning

The ability of pMCC (KY895) and 35 log-phase mutant pMDC (KY895)cultures to produce colonies on acyclovir (“ACV”) or AZT plates wasdetermined in a secondary screen as described below. Briefly, log-phasecultures of TK positive clones were serially diluted in 0.9% NaCl andspread onto acyclovir or AZT plates (TK selection plates except 1 μg/mLthymidine+1 μg/mL acyclovir or 0.05 μg/mL AZT). Mutant cultures werealso spread onto duplicate TK selection and LB+carb50 plates. One set ofTK selection plates and LB+carb50 plates were incubated at 42° C. Allother plates were incubated at 37° C. After 16-24 hours the plates werescored.

Results are shown in Table II below. Briefly, only mutants that gaveresults which differed from those observed with the wild-type pMCC(KY895) are shown. Mutants are designated with the wild-type residue andposition number followed by the amino acid substitution deduced from thenucleotide sequence; e.g.,

F1611 indicates that isoleucine replaces phenylalanine at residue 161 inthis particular mutant. (++) indicates that the same number of colonieswere observed as compared to control plates; (+) indicates that fewer(<20% those observed with pMCC) and generally smaller (˜50% smallerdiameter) colonies were observed as compared to control plates; and (−)indicates that no colonies were observed.

TABLE II Clones ACV AZT LB 37° C. 42° C. pMCC (wild- ++ ++ ++ ++ ++type) P155A/F161V ++ + ++ ++ ++ F1611 + + ++ ++ ++ F161C + − ++ ++ ++F161L ++ ++ ++ ++ − R163P/H164Q + + ++ ++ − F1611/R163H ++ ++ ++ ++ +pMDC − − ++ − −

As shown in Table II, all cultures formed colonies on control TK 25selection and LB+carb⁵⁰ plates. In comparison to the wild-type, severalmutants appeared to preferentially utilize one or both nucleosideanalogues over thymidine (P155A/F161V, F1611, F161C, and R163P/H164Q).In addition, several mutants were unable to form colonies on TKselection plates at 42° C. (F161L and R163P/H164Q), and one(F161I/R163H) showed a severely reduced ability to form colonies at 42°C.

D. Expression of Mutant Enzymes in a Cell-Free Translation System

1. Subcloning of Selected Mutants

In order to study the properties of the mutant TKs, the 1.07 kbp MluI

BssHII fragment of eight mutants was subcloned into the in vitro vectorpT7:HSVTKII. More specifically, DNAs of selected clones were restrictedwith MluI and BssHII to release a 1.07 kbp fragment [nucleotide numbers˜335 through 1400 on the McKnight sequence (Nucl. Acids Res. 8:5949-5964, 1980; the McKnight strain was derived from the mp strain ofHSV-1, Wagner, PNAS 78:1441-1445, 1981)]. The fragments weregel-isolated from 1% agarose gels using GenCleanII, and ligated topT7:HSVTKII vector DNA which had been restricted with MluI and BssHII,treated with calf intestinal alkaline phosphatase, and gel-isolated.pT7:HSVTKII was derived from pT7:HSVTK transcription vector described byBlack and Hruby in J. Biol. Chem. 267:9743-9748, 1992. Briefly,pT7:HSVTKII differs from pT7:HSVTK only by the loss of an NcoI-BamHIfragment 3′ to the end of the HSV-1 tk gene which was originally used toaid in the initial cloning of the tk gene.

2. Sequence Analysis

In the final sequence analysis of the eight mutant fragments subclonedinto the pT7:HSVTKII vector, two additional amino acid differences wereidentified between these tk genes. The sequence of pT7:HSVTKII isexactly the same as that published by McKnight (Nuc. Acids Res8(24):5949-5963, 1980). pMCC, the parental plasmid of pMDC and hence thevector into which the random sequences were ligated, contains two aminoacid aberrations from the McKnight sequence. These are at position 434(C→T) and 575 (G→A), and result in a proline-49 to leucine and anarginine-89 to glutamine change. Therefore, all mutants contain thesetwo mutations in addition to those described. In addition, a singlenucleotide difference at position 480 (C→T) was also identified but doesnot result in an amino acid change.

Because all in vitro analyses were compared against pT7:HSVTKII as thewild-type, the MluI-BssH1I fragment from pMCC was subcloned into thecorresponding sites of pT7:HSVTKII (now designated pT7:MCC) and thesubsequent cell-free translation products compared to those derived frompT7:HSVTKII. Time course and thermal stability analyses showed nosignificant difference between pT7:HSVTKII- and pT7:MCC-derivedtranslation products. No significant difference in phosphorylationefficiency was observed between pT7:MCC and pT7:HSVTKII when thymidine(1.3-fold), deoxycytidine (1.3-fold), GCV (0.8-fold), ACV (0.95-fold),or AZT (1.1-fold) were used as substrate. Furthermore, Sanderson et al.(J. Mol. Biol. 202:917-919, 1988) reported that the K_(m) for thymidineand ATP and the V_(max) of TK purified from E. coli harboring pHETK2(the parent plasmid of pMCC) and HSV-1-infected cells wereindistinguishable. Therefore, the alterations observed in the propertiesof the mutant TKs can be attributed to the nucleotide substitutionswithin the target region and that any differences between the vectors(pT7:MCC and pT7:HSVTKII) exerted only minor changes in catalyticproperties.

3. In Vitro Transcription and Translation

The transcripts described above were then used in a rabbit reticulocytelysate cell-free translation system to synthesize active enzymes.Cell-free translation was according to Promega using nuclease-treatedrabbit reticulocyte lysates.

Expression of full-length proteins was analyzed by subjecting³⁵S-radiolabeled cell-free translation products to SDS-PAGE andautoradiography. Briefly, 1 μl of each radiolabeled cell-freetranslation in vitro-derived mutant mRNAs was subjected toSDS-containing polyacrylamide (12%) gel electrophoresis. Anautoradiograph of this gel is shown in FIG. 7. The first lane contains¹⁴C-labeled rainbow molecular weight markers (Amersham) with theapparent molecular weight (×10⁻³) given on the left. The second lanecorresponds to a cell-free translation performed in the absence of anyadded mRNA. The third lane corresponds to the wild-type pT7:HSVTKII mRNAtranslation product. All other lanes contained translation products ofthe mutant mRNAs produced as described above. As is evident from FIG. 7,the major radiolabeled translation product from each mutant transcriptmigrates during electrophoresis as a ˜43 kDa protein with the sameelectrophoretic mobility as that observed with translation products fromwild-type pT7:HSVTKII transcripts.

To quantitate the level of protein synthesis for each translation,determination of trichloroacetic acid precipitable counts from each ofthe same samples was performed in triplicate. The amount ofacid-precipitable counts roughly parallels the band intensity of eachmutant in FIG. 7.

E. Time Course Analysis of Mutant Enzymes

On the basis of TK activities, mutant TKs were classified into twosubsets: (1) high-activity mutants (P155A/F161V, F161I, F161C, andD162E); (2) low-activity mutants (F161I/R163H, F161L, D162G, andR163P/H164Q). For the high-activity mutant enzymes, unlabeledtranslation products were diluted 1/9 and incubated for 0, 5, 10, 20, or30 minutes at 30° C. Results of this experiment are shown in FIG. 8A:The TK activity results (counts per minute) were adjusted to reflectequivalent protein synthesis levels using the correspondingTCA-precipitable counts (³⁵S cpm). Two of the mutants (F161I andP155A/F161V) demonstrated a statistically higher affinity for thymidinethan the wild-type TK. Standard deviations of F161C and D162E activities(data not shown) indicate no difference in activities when compared tothe wild-type TK enzyme activities.

The low-activity mutants were diluted 1/5, and the rate ofphosphorylation as a function of time was also determined. Results ofthis experiment are shown in FIG. 8B. The time course analysis indicatesthat most of the mutants had less than 10% wild-type activity. One,F161L, however, demonstrated a moderate ability to phosphorylatethymidine, albeit at a much reduced rate from HSVTKII.

F. Thermal Stability Assays

In the assays for colony formation on TK selection plates, severalmutants were unable to complement KY895 at 42° C., suggesting that thesemutant TKs were temperature-sensitive. To substantiate this observation,cell-free translation products were incubated at 42° C. for increasingtimes prior to being assayed for enzyme activity. Briefly, cell freetranslation (“CFT”) products of each high-activity mutant, -RNA, andHSVTKII samples were diluted 1/9 and incubated for 0, 5, 10, and 20minutes at 42° C. The preincubated samples were then assayed for 5minutes (P155A/F161V and F1611) or 20 minutes (-RNA, HSVTKII, F161C, andD162E). The percent of activity remaining was determined with theuntreated samples set at 100%. As shown in FIG. 9A, except for F161C,all high-activity mutants displayed thermal stabilities similar toHSVTKII after 42° C. preincubation periods as long as 60 minutes (datanot shown). Because F161C lost greater than 90% of enzyme activitywithin the first 20 minutes at 42° C., shorter incubation periods at 42°C. were performed (0, 5, 10, and 20 minutes). F161C was exceptionallythermolabile demonstrating a ˜85% activity loss after only 5 minutes at42° C.

Low-activity mutant CFT products were diluted 1/5 and incubated for 0,20, 40, or 60 minutes at 42° C. The preincubated samples were thenassayed in triplicate for the thymidine phosphorylation for 60 minutes.The percent of activity remaining was determined using the untreated(time 0) sample as 100%. As shown in FIG. 9B, for the low-activitymutant subset one translation product (F161L) was more thermolabile thatHSVTKII. Others in this set (R163P, F161I/R163H, H164Q, and D162G) wereequivalent to HSVTKII.

G. Substrate Specificity Assays

Three of the mutants (P155A/F161V, F161I and F161C) were assayed intriplicate for the relative levels of phosphorylation using thymidine,deoxycytidine, ACV, GCV, or AZT as substrates. Briefly, forty-eightmicromoles of each tritiated substrate was used in each assay reaction.Translation products were diluted for each nucleoside assay as follows(translation/H₂O): 1/100, thymidine; 2/3, deoxycytidine, GCV, and AZT;4/1, ACV. Each set of assays was incubated for 2 hours at 30° C. and theamount of phosphorylated product determined.

The counts per minute of each set of assays were adjusted, and plottedas 30 shown in FIG. 10. Briefly, both P155A/F161V and F161I displayed anelevated capacity to phosphorylate thymidine relative to HSVTKII, 2.6-and 2.2-fold, respectively. Phosphorylation of deoxycytidine by themutant enzymes ranged from 1.9- to 2.8-fold over the wild-type enzyme(F1611, 1.9-fold; F161C, 2.8-fold; P155A/F161V, 2.8-fold). Two mutantsappeared to share an increased ability to phosphorylate ACV (2.4- and2-fold over HSVTKII by F155A/F161V and F161C, respectively). All mutantsdemonstrated approximately wild-type levels of AZT phosphorylation. Allmutants assayed appeared to share a large increase in GCVphosphorylation at 3.9-5.2-fold compared to wild-type phosphorylationlevels.

Example 4 Analysis of TK Mutants with Altered Catalytic Efficiencies

In order to identify mutants with altered catalytic activity, 190 of theTK mutants isolated in Example 1 (TKF) were analyzed in the assays setforth below.

A. Colony Formation Ability as a Functional Thymidine Uptake

The protein content of the purified enzymes was estimated by amodification of the Bio-Rad protein assay. A standard curve wasestablished using BSA and 25 μl of Bio-Rad reagent in a final volume of125 ul. The amount of protein was determined by measuring the OD at 595nm and comparing it to that of BSA.

Tn order to identify mutants with altered TK activity, a secondaryscreening protocol was designed based on the ability of the mutants togrow on medium containing different concentrations of thymidine (TableI). Briefly, it was first established that 1.0 and 10.0 μg/mL are theminimum and maximum concentrations of thymidine in the medium thatsupports the growth of E. coli harboring the wild-type tk plasmid. SinceE. coli harboring the wild-type plasmid are unable to form visiblecolonies on TK-selection medium containing low thymidine (0.05 μg/mL),it was postulated that growth at this thymidine concentration might beindicative of mutants with an increased ability to phosphorylatethymidine. Accordingly, 0.05 μg/mL thymidine was used to select forvariants with high TK activity and 20 μg/ml thymidine for variants withlow activity.

Table I below shows the ability of selected mutants to functionallycomplement tk⁻ E. coli KY 895 as a function of increasing thymidineconcentration. When all the 190 TK variants and the wild-type weresubjected to screening at the thymidine concentrations indicated inTable I, only one, TKF 36, formed colonies at the lowest thymidineconcentration tested (0.05 μg/mL). On the other hand, only TKF 41 grewat the highest concentration of thymidine in the medium. All of theother 188 mutants and the wild-type formed visible colonies on mediumcontaining 1 μg/mL thymidine.

TABLE I COLONY FORMING ABILITY OF TK E. COLI KY895 TRANSFORMED WITHWILD-TYPE AND MUTANT PLASMIDS, AS A FUNCTION OF THYMIDINE CONCENTRATIONThymidine concentration (μ/mL)^(a) Mutant 0.05 1 2 10 20 Wild-type _a+a + ±^(b) − TKF 36 + + + ±^(b) − TKF 41 − − + ⁺ +^(c) TKF 52 − + + ⁺ −TKF 99 − + + ⁺ − TKi 208^(d) − + + ⁺ − Colony formation was determinedafter incubation at 37° C. for 24 hours. ^(a)+ and − indicate theability or inability of E. coli harboring different plasmids to formvisible colonies on the indicated TK-selection media. ^(b)± indicatesinitial cell growth: cell death was apparent after incubation for 20hours and may be due to the nucleotide pool imbalance generated byexcessive phosphorylation of thymidine in the mutant and wild-typeclones. ^(c)Since TKF 41 seemed to be a very low activity clone,overexpression of this mutant TK was necessary for the survival of E.coli on TIC-selection medium. pMCC and pMDC expression vectors have atemperature-sensitive repressor gene c1857 which becomes inactive at 42°C. and, hence, there is overexpression of TIC and subsequent cell death.In order to obtain controlled expression, screening was performed at 37°C. However, TKF 41 containing E. coil was incubated at 42° C. on 20μg/mL thymidine containing TK-selection medium. ^(d)TKI 208 was obtainedfrom the library described above in Example 2.

B. Sequence Analysis of High and Low Activity Clone

Wild-type tk and selected mutants were sequenced as described above inExample 2. Table II shows the nucleotide and deduced amino acidsequences of the wild-type tk and selected mutants for codons 165 to175. Briefly, TKF 36, the mutant that forms colonies on lowthymidine-containing medium, contains only a single amino acidsubstitution (Ala168→Ser), whereas TKF 41 contained four substitutions:Pro165→Ser, Ala167→Gly, Leu170→Gln and Ala174→Val. Interestingly, TKF 52has a different amino acid substitution (Ala168→Thr) at the sameposition as TKF 36, but is unable to form colonies on lowthymidine-containing medium. TKF 99 contains two amino acidsubstitutions (Cys 171→Leu and Ala 174→Thi). TKI 208 has a singlenucleotide substitution which results in a Leu170→Val substitution.

TABLE II NUCLEOTIDE AND DEDUCED AMINO ACID SEQUENCES OF THE WILD-TYPEAND MUTANT TK ENZYMES AT THE TARGET REGION SEQ 165a 166 167 168 169 170171 172 173 174 175 ID Wild- ccc atc gcc gcc ctc ctg tgc tac ccg Gcc gcg12 type pro Ile Ala Ala Leu Leu Cys Tyr Pro Ala Ala 13 TKF36 ccc Atc gccTcc ctc ctg tgc tac ccg Gcc gcg 14 Pro Ile Ala SER Leu Leu Cys Tyr ProAla Ala 15 TKF41 Tcc atc gGc gcc ctA ^(b) cAG tgc tac ccg gTc gcg 16 SERIle GLY Ala Leu GLN Cys Tyr Pro VAL Ala 17 TKF52 ccc atc gcc Acc ctg ctgtgc tac ccg gcc gcg 18 Pro Ile Ala THR Leu Leu Cys Tyr Pro Ala Ala 19TKF99 ccc atc gcc gcc TtA ctg tTA tac ccg Acc gcg 20 Pro Ile Ala Ala LeuLeu LEU Tyr Pro THR Ala 21 TKI208 ccc atc gcc gcc ctc Gtg tgc tac ccggcc gcg 22 Pro Ile Ala Ala Leu VAL Cys Tyr Pro Ala Ala 23 ^(a)Shows thecodon number of the target region that was degenerated. The wild-typenucleotide and amino acid sequences are shown below the codon number.^(b)The silent mutations. No other nucleotide changes were observed inthe region sequenced (spanning codons 140-182). Each template wassequenced twice. Substituted nucleotide and amino acid residues areshown in bold capital letters.C. Tymidine Uptake in E. coli HarboringWild-Type and Mutant TK Plasmids

In order to ascertain the actual level of thymidine uptake in E. coliharboring wild-type or mutant plasmids, the following assays wereperformed.

1. [Methyl-³H]thymidine Uptake Assay

[Methyl-³H]thymidine uptake in E. coli harboring wild-type or mutantplasmids was determined essentially as follows. Briefly, overnightcultures of E. coli containing pMDC (inactive TK), a plasmid containingwild-type TK, or TK36 were diluted 1:100 with LB-medium containing 100μg/mL of carbenicillin, grown to 0.1 OD at A₅₅₀, shifted to 37° C. andincubated with vigorous shaking. Once an OD of 1.0 was attained, theculture was brought to room temperature (˜25° C.) and thymidine wasadded to 1.0 mL aliquots at a final concentration of 0.21 μM (0.16 μCi[methyl ³H]thymidine). After incubation for 0, 5, 10, 20, 30 and 60 s at22° C., 50 μl aliquots were transferred onto nitrocellulose filters(0.45 μm), washed under vacuum with 10 mL of chilled 50 mM Tris-HCl, pH7.4, 0.9% NaCl, dried and counted in a scintillation counter usingscintiverse BD (Fisher). Results are shown in FIG. 11. Briefly, therewas essentially no thymidine uptake in E. coli harboring pMDC. Theamount of hymidine uptake in E. coli harboring TKF 36 was 42% greaterthan in E. coli harboring the wild-type plasmid (18 pmol/10⁸ cellscompared to 12.7 pmol/10⁸ after incubation for 10 s).

2. Incorporation of [methyl-³H]thymidine into Acid-Insoluble Material

The amount of TK activity in crude E. coli extracts containing thewild-type and mutant plasmids was determined indirectly by measuring theincorporation of thymidine into acid-insoluble material.

Briefly, cultures were grown as described above under section 1. To 0.5mL of culture, thymidine was added to a final concentration of 1.32 μM(0.2 μCi [methyl-³H]thymidine). A 30 μl aliquot was taken out afterdesignated times of incubation and added to 2.0 mL of cold 5% perchloricacid. The precipitate was washed and radioactivity incorporated into anacid-insoluble material was determined essentially as described by Dubeet al., 1991.

FIG. 12, shows that the incorporation of [methyl-³H]thymidine into anacid-insoluble product is more rapid with TKF 36 E. coli than with E.coli harboring the wild-type plasmid or the other tk mutants tested. Oneof the mutants, TKF 99, having two amino acid substitutions (Cys171→Leuand Ala174→Thr) exhibited the same rate of thymidine incorporation asdid the wild-type. TKF 52 contains an Ala168→Thr substitution (compareAla168→Ser in TKF 36) and is unable to form colonies in the lowestthymidine-containing TK-selection medium (Table I), yet incorporatesthymidine into acid-insoluble material at a rate greater than that ofwild-type but less than that of TKF 36.

D. Purification of Wild-Types and Mutant TKS

Crude extracts of the different mutants were obtained from 11 culturesthat were grown at 30° C. to 0.1 OD at A₅₅₀, shifted to 37° C. and grownto 1.0 OD. The cells were harvested by centrifugation at 4° C., washedwith 25 mL of a solution containing 25% (w/v) sucrose, 50 mM Tris-HCl,pH 7.5, and 5 mM EDTA. After centrifugation the cell pellet (˜5-6 gweight) was stored at −70° C. The cell pellet was thawed and suspendedin 20 mL of buffer I (buffer I consisted of 10 vol. 50 mM Tris-HCl, pH7.5, 10% sucrose mixed with 1 vol. 0.3M spermidine-HCl, 2.0M NaCl, 10%sucrose and 0.5 mM PMSF, pH 7.5). Once resuspension was uniform, 4.0 mLof buffer I containing 6.25 mg of lysozyme was added. The suspension waspoured into a chilled centrifuge tube and placed on ice for 30 minutes.If cells did not lyse thin 30 minutes, the tube was placed in a 37° C.waterbath for 4-6 minutes to enhance lysis. Once cells started to lyseas judged by increasing stringiness, 2-3 mL of chilled buffer Icontaining 50 μg/mL aprotinin and 2 μg/mL of each leupeptin andpepstatin, was added to a final volume of 25 mL and the mixture wascentrifuged at 28,000 r.p.m. for 1 hour at 4° C. and the supernatant wasstored at 70° C.

The wild-type and mutant TKs were purified by affinity chromatography ona matrix of p-aminophenylthymidine 3′-phosphate coupled to CH-Sepharose4B (Pharmacia) as described by Kowal and Marcus (Prep. Biochem.6:369-385, 1976) with modification by Lee and Cheng (J. Biol. Chem.251:2600-2604, 1976). All buffers used in the purification of TKcontained 5 mM DTT, 50 μ/mL aprotinin, 2 μg/mL each of leupeptin andpepstatin and 1 mM PMSF unless otherwise indicated. A 7 mL bed-volumecolumn was equilibrated with buffer A (0.1 M Tris-HCl, pH 7.5, 10%glycerol) and then loaded with ˜25 mL of the unfractionated supernatantat a rate of 8-10 mL/h. The column was recirculated with theflow-through twice and then washed sequentially with ten bed-volumeseach of buffer B (0.1 M Tris-HCl, pH 7.5, 0.5 M KCl, 10% glycerol)followed by buffer A. TK was eluted with a linear gradient of thymidine(0-600 μM) using 30 mL each of buffer A and buffer C (0.3 M Tris-HCl, pH7, 4, 50 mM KCI, 10% glycerol). TK assay was performed on all thefractions and peak TK fractions were pooled and dialyzed against threechanges of 21 of dialysis buffer (50 mM Tris-HCl, pH 7.4, 5 mM DTT, 10%glycerol). In the final dialysis, protease inhibitors were omitted fromthe buffer and the dialyzed fractions were aliquoted and stored at −70°C. The column was washed thoroughly twice by using the same washing andelution protocols as described above prior to application of eachextract preparation.

The protein content of the purified enzymes was estimated by amodification of the Bio-Rad protein assay. A standard curve wasestablished using BSA and 25 μl of Bio-Rad reagent in a final volume of125 ul. The amount of protein was determined by measuring the OD at 595nm and comparing it to that of BSA.

[Methyl-3H]thymidine Uptake

Results are shown in FIG. 11. Briefly, there was essentially nothymidine uptake in E. coli harboring pMDC. The amount of thymidineuptake in E. coli harboring TKF 36 was 42% greater than in E. coliharboring the wild-type plasmid (18 pmol/10⁸ cells compared to 12.7pmol/10⁸ after incubation for 10 s).

The amount of TK activity in crude E. coli extracts containing thewild-type and mutant plasmids was determined indirectly by measuring theincorporation of thymidine into acid-insoluble material.

E. Kinetic Parameters of Purified Mutant Thymidine Kinases

The three cellular parameters so far studied suggest that TKF 36 is amore active enzyme than any of the other mutant enzymes tested or thewild-type. In order to determine the kinetic parameters of catalysis,wild-type, TKF 36 and three other mutant thymidine kinases were purifiedto near homogeneity using affinity chromatography as described above.The purified wild-type, TKF 36 and TKI 208 were examined byelectrophoresis in an SDS-PAGE system and were found to exhibit a singleprominent band that migrated at 43 kDa, which was judged to be 95%homogeneous by silver staining.

Kinetic parameters were determined essentially as described below.Briefly, TK assay mixtures (50 μl) contained 50 mM Tris-HCl, pH 7.5, 5mM ATP, 4 mM MgCl₂, 2.5 mM DTT. 12 mM KCl, 018 mg/mL BSA, 5% glycerol, 1μM thymidine (0.3 μCi [methyl-³H]thymidine) and the indicated amounts ofpurified enzymes. The kinetics of thymidine phosphorylation weredetermined by varying the unlabeled thymidine concentration (0-4.0 μM)and known amount of purified enzymes (the sp. acts of the purified TKswere 1.1, 3.0, 0.5, 0.34 and 0.01 units for wild-type. TKF 36, TKI 208,TKF99 and TKF41, respectively). One unit of enzyme is defined as theamount that phosphorylates 1.0 pmol of thymidine to thymidylic acid in 1minute under the conditions described above. Incubation was at 34±1° C.for 10 minutes. The reaction was stopped by the addition of 1 mM coldthymidine. Half of the reaction mix was pipetted onto a DEAE-cellulosedisc (25 mm) and the disc was dipped in distilled water (1 minute)followed by four washes each in 10 mL of absolute ethanol. The adsorbedproducts on the disc were counted in a scintillation counter. Thekinetic parameters K_(m) and V_(max) were determined by using theCleland SUBIN program (Cleland, Methods Enzymol. 63:103-138, 1979) andthe values for k_(cat) were calculated from the equationV_(max)=k_(cat)[E]o, where [E]o is the total enzyme concentration.

Results of these assays are summarized in Table III. Ala168→Sersubstitution in TKF 36 resulted in a 4.8-fold enhancement in k_(cat).None of the other purified mutant enzymes (TKF 41, TKF 99 and TKI 208)that were analyzed exhibited an increase in k_(cat) compared to that ofthe wild-type TK. A 2.2-fold decrease in k_(cat) results form theLeu170→Val substitution in TKI 208, whereas two of the other tk mutants,TKF 99 and TKF 41, with decreased efficiencies in the in vivo assays,exhibited a 28- and 34 700-fold decrease in k_(cat). Table III alsopresents the Michaelis constant (K_(m)) for the mutants and wild-typewith thymidine as a substrate. The apparent K_(m) for the wild-typeenzyme was 0.47 μM, which agrees well with previously reported values(Jamieson and Subak-Sharpe, J. Gen. Virol. 24:481-492, 1974; Elion, Am.J. Med. 73:7-13, 1982; Waldman et al., J Biol. Chem. 258:11571-11575,1983). Even though TKF 36 showed a higher k_(cat) value its affinity forthymidine, as reflected in the K_(m), is 6.2-fold lower than thewild-type TK. TKI 208, TKF 41 and TKF 99 have a similar K_(m) to that ofthe wild-type. Interestingly, the k_(cat)/K_(m) value of TKF 36 [2.0×10⁶s⁻¹M⁻¹] is not very different from the wild-type [2.5×10⁶ s⁻′M⁻¹], whileTKI 208, TKF 99 and TKF 41 exhibit lower values of 1.57×10⁶, 0.15×10⁶and 0.00012×10⁶ s⁻¹M⁻¹, respectively.

TABLE III COMPARISON OF KINETIC PARAMETERS OF THE THYMIDINE KINASESEnzyme K_(m) (μM) k_(cat) (^(1/s)) Wild-type 0.47 ± 0.1^(a) 1.2 TKF 362.90 ± 0.01 5.7^(b) TKF 41 0.28 ± 0.16 3.5 × 10^(−5b) TKF 99 0.29 ±0.002 0.04^(b) TM 208 0.35 ± 0.008 0.5^(b) ^(a)Data presented as ± SE.^(b)The P value is <0.02 compared to the wild-type.

Example 5 Selective Killing of Cells Transfected with Retroviral VectorsContaining Mutant HSV-1 TK

The example describes the construction of retroviral vectors whichexpress a type 1 Herpes Simplex Virus thymidine kinase, a proline toalanine mutation at position 155, and a phenylalanine to valine mutationat position 161.

A. Vector Construction

The thymidine kinase gene from P155A/F161V is utilized to replace thewild-type HSV tk sequences in the Moloney Murine Leukemia Virus(“MoMLV”) based vector G1TkSvNa.90 from Genetic Therapy, Inc.(Gaithersburg, Md.; see Ram et al. Cancer Research 53:83, 1993). Inparticular, the mutant tk gene is inserted downstream from the 5′ longterminal repeat sequence, which the tk gene uses as a promoter. Thisvector also contains an neomycin phosphotransferase gene (neo) which isexpressed from an SV40 early promoter.

B. Producer Cell Line

The retroviral vectors described above may then be packaged by theamphotropic retroviral packaging cell line GP+envAml2 (U.S. Pat. No.5,278,056) after calcium phosphate transfection. A vector containing thegene for β-galactosidase is used as a control vector. The cloned vectorproducer cells are maintained in culture containing Dulbecco's modifiedEagle's medium with 10% fetal calf serum, 2 mM glutamine, 50 units/mlpenicillin, 50 μg/ml streptomycin and 2.5 μg/ml Fungizone. Prior toadministration, the media is removed and the cells rinsed with saline.The monolayers are trypsinized for 5-10 minutes at 37° C., collected,washed twice and resuspended at 5-10×10⁸ cells/ml.

C. In Vitro Sensitivity to Ganciclovir

To assess the sensitivity of cells transduced with the mutant or thewild

type tk gene containing vectors, rat 9L glioma cells and human U251glioblastoma cells are transduced in vitro by exposing the cells tosupernatant containing replication incompetent vector particles. Thetransduced cells are selected by including G148 (1 mg/ml) in the culturemedium. Nontransduced, HSV tk wild-type transduced and HSV tk mutanttransduced cells are then evaluated for their sensitivity to increasinglevels of ganciclovir. The level of DNA synthesis is determined bytritiated thymidine incorporation after various ganciclovir exposuretimes and ganciclovir levels. Cell viability is determined by platingthe cells in 10 cm tissue culture plates in the absence or presence ofvarious ganciclovir concentrations, and counting the number of cells at24 hour intervals.

D. In Vivo Transduction

The efficiency of in situ transduction of and relative level of vectorgene expression in the tumor cells is determined using theβ-galactosidase containing vector. Briefly, Fischer 344 rates areanesthetized and injected with 4×10⁴ syngeneic 9L gliosarcoma cellsusing a 10 μl Hamilton syringe connected to a stereotaxic injectionapparatus. After ten days, the same stereotaxic position is used todirectly inject. 1.5×10⁶, 3×10⁶ or 6×10⁶ HSVtk (wild-type or mutant)β-galactosidase transduced or nontransduced producer line cells, andproducer cell line supernatants into the 9L tumor. As a control, ratsare injected with the same volume of sterile saline instead of cells.Ganciclovir is then administered and the rats are sacrificed todetermine the anti-tumor effect. A histological examination is alsoperformed.

E. Dose Optimization of Ganciclovir

Rats are injected intracerebrally with 4×10⁴ HSVtk (wild-type or mutant)or (β-galactosidase transduced rat 9L producer cells. Seven days postinoculation, ganciclovir is administered i.p. at 5, 20 or 15 mg/kg twicedaily for 7 days. Control rats receive i.p. saline injections. All ratsare sacrificed after the ganciclovir treatment and the brains and tumorsremoved for weight determination and histological examination.

F. Tumor Regression with Wild-type and Mutant HSV tk Transduction andGCV

Based on the results of the ganciclovir dose optimization, rat tumorsinoculated with transduced or nontransduced producer cells or producedcell supernatant are administered ganciclovir doses for a specific timeperiod. Antitumor effects are determined by determination of tumorweight and histological examination.

Example 6 The Use of VZV TK Mutants as Targets for Selectable HomologousRecombination

This example describes the use of a mutant Varicella Zoster Virusthymidine kinase (“VZV tk”) as a target for homologous recombination inthe construction of stable transfected cells lines, strains orrecombinant viruses. In particular, the construction of vaccinia virusesas cloning vectors containing mutant VZV TKs for the selection ofrecombinant viruses in TK⁺ cell lines is described.

A. Construction of Recombinant Vaccinia Virus Plasmids Containing VZV TKMutants

VZV tk genes (wild-type and mutant) are cloned into a recombinantplasmid behind the vaccinia virus 7.5 K promoter for constitutive geneexpression. In addition the neomycin phosphotransferase gene is clonedafter the 3′ end of the VZV tk gene to serve as a selectable marker. The5′ or 3′ regions of the vaccinia virus encoded thymidine kinase geneflanks the 5′ end of VZV tk gene and the 3′ end of the neomycinphosphotransferase gene (neo). This allows for the insertion of the VZVtk gene into the viral genome and the concomitant inactivation of thevaccinia thymidine kinase gene. The remainder of the plasmid is based onpUC and contains an ampicillin resistance gene and a ColE1 origin ofreplication for maintenance of the plasmid in E. coli.

B. Construction of Recombinant Poxviruses

The VZV tk (wild-type or mutant)+neo recombinant plasmid or recombinantplasmid containing only the neo gene is cotransfected with the wild-typevaccinia virus into BSC40 cells. Recombinant viruses are selected byresistance to G418. After several rounds of plaque purification, therecombinant viruses are subjected to plaque hybridization and DNAanalysis in order to confirm the insertion and location of the foreigngenes.

C. Dose Optimization of Ganciclovir

Vaccinia virus infected and uninfected BSC40 cells are subjected totreatment with various doses of ganciclovir in order to determine thetolerance level. Cells infected with recombinant viruses expressing VZVTKs and neo or those expressing only neo will be grown in the presenceof various levels of ganciclovir. VZV tk gene containing viruses aremore sensitive to ganciclovir treatment than the cells alone or thoseinfected with wild-type vaccinia virus. A level of ganciclovir isselected from the results of this experiment to select for the loss ofsensitivity to ganciclovir for homologous recombination with other genesto be inserted into the VZV tk locus.

D. Selection of Recombinant VZV tk Poxviruses Using Ganciclovir

BSC40 is infected with the VZV tk recombinant virus in the presence of arecombinant plasmid carrying the gene to be introduced into the VVgenome, abutted to the VV 7.5 K promoter cloned with VZV tk sequencesflanking. Recombinant virus is selected with ganciclovir.

Any cell line stably transfected with the VZV tk gene can be the targetfor introduction of foreign genes by homologous recombination and forthe selection of such an event by resistance to ganciclovir.

Example 7 Construction and Analysis of HSV-1 Thymidine Kinase and HSV-1DNA Polymerase Vectors A. Construction of Vectors

Three constructs were made containing either the HSV-1 DNA polymerasegene, HSV-1 thymidine kinase gene or both.

a) pHSG576:HSVpol

The 5.5 kb HinDIII/EcoRI fragment from pGEM2-702 (David Dorsky, Univ. ofConn.) was cloned into pHSG576 (Sweasy and Loeb, J. Biol. Chem267:1407-1410, 1992) in two steps:

-   -   1) The 2.4 kb PstI/EcoRI fragment was cloned into pHSG576igested        with Pstl and EcoRI. This clone was designated pHSG576: 1/2 pol.    -   2) The 3.1 kb HinDHI/Pstl fragment of HSV DNA polymerase was        cloned into pHSG576:1/2 pol digested with HinDIII and PstI. This        clone was designated pHSg576:HSV DNA pol.

b) pHSG576:HSV-1 TK

The XbaI/BamIII fragment from pET23d:HSVTK (contains the HSV-1 TKNcol-Ncol fragment in pET23d, Novagen) was blunt-ended and cloned intothe SmaI site of pHSG576. The clone was designated pHSG576:HSV-1TK.

c) pHSG576:HSV pol/TK

This clone contains both the HSV-1 DNA polymerase and TK genes forcoexpression from the same vector. It was created in a two step cloningprotocol.

-   -   1) The XbaI/BamHI-bluntended TK fragment was cloned into the        bluntended EcoRI site of pHSG576:1/2pol (contains the 2.4 kb        PstI/EcoRI fragment).    -   2) The 3.1 kb HinDIII/PstI fragment (5′ end of the polymerase        gene) was cloned into pHSG576:1/2pol/TK digested with HinDIII        and PstI. This clone was designated pHSG576:HSVpol/TK.        B. Transformation of E. coli with a DNA Polymerase Defect

E. coli JS200 (polAl2recA718) was transformed with pHSG576:HSV DNA polor pHSG576 DNA and plated on nutrient agar (NA) containing tetracycline(12.5 μg/mL) and chloramphenicol (34 μg/mL). Plates were incubated at30° C. (permissive temperature). Single colonies were grown overnight inNB+tet+Cm. DNA was isolated from these cultures and used to transformJS200 again. From the second transformation several colonies from eachwere picked and used to inoculate NB 30+tet+Cm in the presence orabsence of IPTG. After overnight growth at 30° C., a single loopful ofeach culture was spread in a diverging spiral of increasing dilutionfrom the center of the plate. NA plates+tet+Cm+/−IPTG were incubated at30° C. (permissive) or 37° C. (nonpermissive).

The growth pattern of cells containing pHSG576:HSV DNA pol displayedgrowth of single colonies (low cell density) at 37° C., while cellscontaining only the vector were unable to grow at low cell density atthe nonpermissive temperature.

These results demonstrate that the Herpes DNA polymerase can complementthe E. coli Poll defect in vivo.

Example 8 Construction and Analysis of TK Mutants with Mutations atCodons 159 to 161 and 168 to 170 Utilizing a 100% Random Library

This example describes the construction and analysis of TK mutants thatare mutagenized at codons 159 through 161 and 168 through 170.

Bacterial Strains. SY211 (BL21(DE3) tdk⁻, pLysS) is cured of pLysS byrepeated passages on non-selective plates (no chloramphenicol). (SY211is a gift from William Summers, Yale University, New Haven, Conn. and isdescribed in Summers, W. C. and Raskin, P., J. Bact. 175:6049-6051,1993). The resulting strain BL21(DE3) tdk is used in the geneticcomplementation assays for thymidine kinase activity. Other strains usedare described in Example 3.

Cells. BHK tk-(ts13) cells (ATCC No. CRL-1632) are purchased from theAmerican Type Culture Collection and cultured in DMEM+10% calf serum at37° C. under 6% CO₂.

Materials. As described in Example 3.

A. Generation of TK Mutants

1. Construction of Random Insert

Two oligonucleotides are synthesized by Operon (Alameda, Calif.): MB 126(58 mer) 5′-TGGGAGCTCA CATGCCCCGC CCCCGGCCCT CACC NNNGACCGCC ATCCCATC-3′(SEQUENCE ID No. 24) and MB127 (51 mer) 5′-ATAAGGTACC GCGCGGCCGGGTAGCANNNN NNNNNGGCGA TGGGATGGCG G-3′ (SEQUENCE ID No. 25). The Ndesignates an equimolar mix of all four nucleotides during synthesis.

The purification of oligonucleotides, annealing, extension and 10amplification by PCR is essentially as described in Example 3.

2. Generation of Random-Sequence Containing Libraries VectorConstruction

pET23d, purchased from Novagen, is the backbone for the construction ofpET23d:HSVTK-Dummy. pET23d:HSVTK-Dummy is used in place of pMDC(described in Example 1 and 3) for insertion of random sequences.Briefly, a 1.7kb NcoI/HinDIII fragment is purified from a restrictiondigest of pT7:HSVTKII (Example 3) and cloned into pET23d restricted withthe same enzymes to generate pET23d:HSVTK. The dummy vector isconstructed by replacing the tk sequences between the Kpnl and SacIsites with the KpnI/SacI fragment from pMDC (Example 3).

Library Construction

Qiagen column purified pET23d:HSVTK-Dummy DNA is restricted with KpnIand SacI and the vector gel isolated using GenCleanII (Bio101, La Jolla,Calif.) to remove the small insert fragment. This vector is ligated withthe gel isolated PCR-amplified random fragment overnight at 16° C. withT4 DNA ligase.

3. Selection of TK Mutants

The ligated mixture is then used to transform BL21(DE3) tdk cells byelectroporation as described in Example 3. The transformants are plateddirectly onto TK selection plates (Example 3) with a small fractionplated on 2× YT (16 g tryptone/10 g yeast extract/5 g NaCl/15 gBactoAgar per liter)+carbenicillin at 50 μg/ml (carb⁵⁰) to determine thetotal number of transformants. The plates are incubated at 37° C.overnight and scored for growth on TK selection plates and thetransformation frequency determined. Colonies that grew on the TKselection plates are picked and restreaked on fresh TK selection platesand 2× YT+carb⁵⁰ plates. Approximately 426 positive clones areidentified from a library of 1.1×10⁶ transformants or 0.039% of alltransformant conferred TK activity to E. coli BL21(DE3) tdk (FIG. 14).

B. Analysis of Mutants

1. Sequence of Selected and Unselected Clones

Seventeen clones that demonstrated TK activity (selected) or are takenfrom 2× YT+carb⁵⁰ plates (unselected) are successfully sequenced. DNA isisolated using Qiagen miniprep kits and subjected to double strandsequencing as described in Example 3. FIG. 15 shows the sequences fromeach group and demonstrates that the initial random oligonucleotides arerandomized. In both selected and unselected tk genes, the introductionof secondary mutations at sites distal to the randomized region areobserved. However, the mutations are primarily confined to two codons,155 and 156. These mutations are most likely introduced by contaminationduring the synthesis of the original random oligonucleotides. Allchanges at codon 155 are silent. Changes at codon 156 resulted inalanine to valine, serine or proline alterations. Alignment studiesindicate that position 156 is not conserved either for alanine nor forthe type of amino acid at that position. Therefore, it is unlikely thatthese secondary mutations result in any real effect on the enzymeactivity of the mutants. All selected mutants contained at least twoamino acid changes.

2. Secondary Screening for GCV and ACV Sensitivity

Each of the 426 mutants is picked and used to inoculate 200 μl of TKselection medium (Example 3) in a 96 well microtiter plate format. All426 clones are then serially diluted 10⁴ in 0.9% NaCl with a 48-prongreplicator (Sigma, St. Louis, Mo.). 30 μl of the last dilution is spreadonto TK selection plates containing 1 μg/ml thymidine plus varyingconcentrations of ganciclovir or acyclovir. Initially 2 μg/ml GCV isused and the clones unable to grow are scored as positives since anymutant with increased conversion of a pro-drug to an active toxinresults in lethality. On 2 μg/ml GCV 197 clones are identified.Sequential plating on 1 μg/ml and 0.5 μg/ml GCV lead to theidentification of 47 mutants. Plating on ACV plates (1 μg/ml) gave 116ACV sensitive clones. To ensure that the clones are truly sensitive tothe nucleoside analog and not simply scored because of the inability togrow on the lower thymidine concentrations used, the 47 GCV and 116 ACVclones are plated on TK selection plates containing thymidine at 1 μg/ml(no nucleoside analog). Almost half of the clones are unable to grow onlow thymidine for a total of 26 GCV sensitive mutants and 54 ACVsensitive mutants. Results are shown in FIG. 16.

C. In Vitro Analysis

1. In Vitro Transcription and Translation.

Plasmid DNA is purified by Qiagen column chromatography. Transcriptionand translation of the 80 selected mutants is done as in Example 3except that the isolated plasmids are not linearized prior totranscription. In vitro translation products are assayed in duplicatefor thymidine, ganciclovir and acyclovir phosphorylation and compared topET23d:HSVTK mRNA translation product assays (see Example 3).

2. Measurement of Enzyme Activity

Radiolabelled nucleosides are present in each assay at 1 μM, 7.5 μM and7.5 μM for thymidine, ganciclovir and acyclovir, respectively. The levelof activity is adjusted to reflect the level of protein synthesis asdetermined from the TCA precipitable counts from a duplicatedtranslation with ³⁵S methionine. For the majority of the 80 mutantenzymes, the level of thymidine, ganciclovir and acyclovir is less that1% that of the wild-type TK. Ten mutant enzymes displayed greater that10% phosphorylation with at least one of the nucleosides assayed. Thenucleotide sequences are shown in FIG. 17. Several of the clonescontained mutations outside the randomized region. Two clones, 30 and84, have mutations that result in amino acid changes, A152V and A156S,respectively. Four clones contain in-frame deletions; three (226, 340and 411) with −3 deletions and one (197) with a −6 deletion. All thesemutations are centered around a GC-rich region which encodes for, thepeptide A P P P A. This proline rich peptide is likely to comprise aturn at the tip of a loop section. The loss of one or two, amino acidsmay simply result in shortening of the loop. All of these mutantscontain three to six amino acid alterations within the randomized regionas shown in FIG. 18 with the respective levels of activity determined invitro.

D. Effect of GCV and ACV on Mammalian Cells Expressing Mutant ThymidineKinases

1. Subcloning into a Mammalian Expression Vector

Three mutant thymidine kinases are selected to evaluate for celltoxicity in vivo in the presence of ganciclovir or acyclovir. Mutantclones number 30, 75 and 132 and the wild-type thymidine kinase genesare restricted with NcoI and blunt-ended with Klenow. The gel isolatedfragments (NcoI-blunt) are ligated to pCMV restricted with NotI andtransformed into E. coli strain NM522. The wild-type TK gene in thewrong orientation relative to the CMV promoter is also used as acontrol. Qiagen column purified clones are sequenced to confirmorientation, sequence and the 5′ junction region. The clones aredesignated pCMV, pCMV: TK-wrong, pCMV: TK, pCMV:30, pCMV:75 andpCMV:132.

2. Transfections

As an initial step to evaluate these mutants, the pCMV clones areintroduced in the presence of a neomycin resistant marker plasmid(pSV2neo) into TS 13 BHK tk⁻ cells (baby hamster kidney cells) bycalcium phosphate precipitation using a modified version of Chen andOkayama (Molec. Cell. Biol. 7:2745-2752, 1987).

Briefly, the cell transfections are performed as follows. Approximately5×10⁵ ts13 BHK tk⁻ cells (ATCC CRL-1632) are plated on 100 mm dishes inDMEM+10% calf serum. For each transfection 1 μg of pSV2neo and 10 μg ofa pCMV construct (pCMV, pCMV:TK-wrong (HSVTK in the wrong orientationrelative to the promoter), pCMV:HSVTK, pCMV:30, pCMV:75 or pCMV:132 DNA)in 0.25M CaCl₂ are mixed with 0.5 ml 2× BBS (see Chen and Okayama) andpreincubated at 37° C. at 2.5% CO₂ for 24 hours. The CaCl₂/DNA mix isadded dropwise to the plates and mixed in well. After a 24 hourincubation at 37° C. in a 2.5% CO₂ wet incubator, the cells are rinsedtwice with Dulbecco PBS minus Ca/Mg and fed with fresh DMEM+10% calfserum. Plates are incubated at 37° C. with 6% CO₂. After 72 hourspost-transfection the cells are split 1:3 and plated in DMEM+10% calfserum containing G418 at 600 μg/ml.

3. Selection and ED₅₀ Determinations

The cells are selected on G418 (600 μg/ml) at 37° C. for 17 days. Duringthis time the plates are pooled (for each DNA transfection) and splitthree times at a ratio of 1:3. Approximately 30-40 clones are selectedin this manner for each transfected DNA containing a tk gene in thecorrect orientation. The pCMV and pCMV:TK-wrong transfections yieldedbetween 130 and 140 clones each. G418 resistant clones are harvested,pooled and plated at a density of 2000 cells/well in 100 μl DMEM+10%calf serum and 200 μl/ml G418+6% CO₂ in 96 well microtiter plates. Aconcentration range of either ganciclovir (0.125, 0.25, 0.5, 1, 2.5, 5,7.5, 10 and 20 μM) or acyclovir (0.5, 1, 2.5, 5, 10, 25, 50, 75 and 100μM) is added to each plate with 8 repeats of each concentration for eachtransfectant population (the no nucleoside analog controls each had 16repeats). After three days in the presence of the nucleoside analog,Alamar Blue is added and 6 hours later the plates are scanned using afluorometer as according to the manufacturer's protocol (AlamarBiosciences, Inc., Sacramento, Calif.). The plates are incubated afurther 24 hours at 37° C. and scanned again.

Determination of the fluorescence level of cells incubated in thepresence of Alamar Blue directly relates to cell viability. Subtractionof the background fluorescence allows one to plot the cell survivalversus the nucleoside analog concentration to determine to effectivedose for killing 50% of the cells (ED₅₀). The survival curves areplotted with data from the second scan and are shown in FIGS. 19 (GCV)and 20 (ACV).

After 4 days on nucleoside analog the effective doses for 50% cellkilling with GCV and ACV are determined from FIGS. 19 and 20 (see TableIV).

TABLE IV ED₅₀ fold over ED₅₀ fold over GCV WT ACV WT WT 20 μM 1 25 μM 130 4.4 μM  4.5 18 μM 1.4 75 0.47 μM   43 1.25 μM   20 132  18 μM 1.1 25μM 1

4. Enzyme Assays and Immunoblots

Cell extracts from 2.4×10⁶ pooled transfectants are assayed forthymidine, ganciclovir and acyclovir activity. The levels ofphosphorylation corresponded very well with the activities determined invitro (rabbit reticulocyte lysate translation products) and the amountof protein expression as determined by western blot analyses. Noimmunoreactive band is seen in the lanes corresponding to pCMV orpCMV:TK-wrong (TK gene in the wrong orientation). Both the wild-type TK(pCMV:HSVTK) and pCMV:132 transfected cell lysates exhibited roughlyequivalent band intensities. The immunoreactive band for pCMV:30 celllysates is substantially more intense (5-10 fold) and that of pCMV:75 isapproximately half the pCMV:HSVTK band intensity for the equivalent cellnumber.

5. Testing Mutants in Glioblastoma Cell Lines

Blunt-ended NcoI fragments isolated from pET23d:HSVTK, pET23d:30 andpET23d:75 are cloned into the HpaI site of pLXSN (Miller and RosmanBioTechniques 7:980, 1989). Plasmid purification is done by Qiagenchromatography and the isolated DNA sequenced to confirm orientation and5′ junction regions. Stable transfectants of rat C6 glioblastomas (ATCCCCL-107) and a human glioblastoma cell line (SF767) are made asdescribed above with the exception that pSV2-neo is not co-transfectedsince the neomycin phosphotransferase gene is encoded by pLXSN.Selection and analysis is essentially as described above.

E. Kinetic Analysis of Mutant Thymidine Kinases

1. Overexpression of Mutant and Wild-Type Enzymes

A single colony of pET23d:HSVTK, pET23d:30, pET23d:75 and pET23d:132 inBL21(DE3)tk cells is used to inoculate 5 ml of M9ZB medium (1% tryptone,0.5% NaCl, 1×M9 salts, 1 mM MgSO₄, 100 μM CaCl₂ and 0.2% glucose)containing cabenicillin at 20 μg/ml. The culture is incubated at 37° C.overnight. The following day the 5 ml culture is used to inoculate 1LM9ZB+cabenicillin at 20 μg/ml and the culture allowed to grow at 37° C.to OD600 0.1. At that point IPTG is added to 0.4 mM and the cultureincubated a further 3 hours. The cells are chilled on ice, pelleted bycentrifugation and the pellets washed once in cell wash buffer (50 mMTris, pH 7.5, 5 mM EDTA, 10% sucrose) prior to freezing the pellets at−70° C. The next day the cells are resuspended in 12 ml Buffer 1 (50 mMTris, pH 7.5, 10% sucrose, 2 mM DTT, 5 mM EDTA, 1 mM PMSF) and thevolume split into two 13 ml Oakridge ultracentrifuge tubes. 1 ml Buffer1 containing 3 mg lysozyme is added to each tube and the tubes left onice for 1 hr. An additional 1 ml Buffer 1+protease inhibitor mix isadded and the tube spun at 35 krpm in a Sorvall T-1250 rotor at 4° C.The cleared supernatant is then aliquoted and frozen at −70° C.

2. Affinity Purification

A thymidylyl-sepharose column is used for a one step purificationprocedure (see Example 2). The 1 ml bed volume column is prepared bypassing 10 ml Buffer 1 followed by 10 ml Absorption Buffer (50 mM Tris,pH 7.5, 10% sucrose, 2 mM DTT, 25 mM MgAc₂, 10 mM ATP) over the column.Two ml of the cleared lysate is mixed with 2 ml of Absorption Buffer andpassed through a 0.2 μm filter. This mix is passed over the column 3times. The column is washed with 5 ml Absorption buffer three times andthe 5 ml fractions collected. To elute the enzyme, 3-1 ml fractions ofThymidine Buffer (300 mM Tris, pH 7.5, 10% sucrose, 2 mM DTT, 50 mM KCl,600 μM thymidine) is passed over the column and each 1 ml fractioncollected. The column is reactivated by loading on 10 ml High SaltBuffer (50 mM Tris, pH 7.5, 10% sucrose, 2 mM DTT, 0.5M KCl) and 10 ml50 mM Tris, pH 7.5. The column is stored in 50 mM Tris pH 7.5+0.004%sodium azide. The extent of purification is monitored by Coomassiestained SDS:PAGE analysis and the concentration of purified proteindetermined using the BioRad Reagent (Bradford Reagent). The fractioncontaining TK protein is dialyzed against several liters of 50 mM Tris,pH 7.5 10% sucrose, 2 mM DTT at 4° C. to remove thymidine.

3. Enzyme Kinetics

The kinetics of thymidine, ganciclovir and acyclovir phosphorylation bythe wild-type, mutant 30 and 75 thymidine kinase enzymes with variantconcentrations of radioactive nucleoside substrate are determinedessentially as described in Example 3. K_(m) and V_(max) values aredetermined from double reciprocal plots and kcat values are calculatedusing the equation V_(max)=k_(cat) [E_(o)] where [E_(o)] is the totalenzyme concentration. The BioRad reagent was used to determine the totalenzyme concentration of purified thymidine kinase enzymes. Results areshown below in Table I.

TABLE V Kinetic characterization of HSV-1 TK Mutants with thymidine, ACVand GCV as substrate Substrate thymidine ganciclovir acyclovir EnzymeW.T. 75 30 W.T. 75 30 W.T. 75 30 K_(m) (μM) .380 .950 13.3 47.6 10.0 333417 23 455 k_(cat) (sec⁻¹) .230 .210 .003 .050 .050 .009 .008 .010 .001k_(cat) (sec⁻¹) .60 .22 2E−4 1E−3 4.8E−3 2.7E−5 1.8E−5 4.5E−4 2.1E−6K_(m) (μM) *Calculations of k_(cat) are per active site

Example 9 Production of Second-Generation HSV-1 Thymidine Kinase Mutantshaving Amino Acid Substitutions in Residues 159-161 and 168-169

This example describes the construction and analysis of a secondgeneration of TK mutants, which are mutagenized at codons 159-161 and168-169.

A. Isolation of Second Generation TX Mutants

As described above, mutants isolated from the LIF-ALL library showincreased prodrug specificity compared to the wild-type TK (see also,Black et al., Proc. Nat'l Acad. USA 93:3525-3529, 1996). Usinginformation from the ten most active mutants isolated from the LIF-ALLlibrary, a new set of randomized oligonucleotides were synthesized andused to generate a second generation random library. Since the librarywas skewed to mutagenize codons encoding residues 159-161 and 169-170 toonly represent a few amino acid substitutions, the library is consideredto be semi-random.

FIG. 21 shows the semi-randomized oligonucleotides used to generate thelibrary and the possible amino acid substitutions expected. Thesecomplimentary and partially overlapping oligonucleotides (DMO2211 and2212) were purified after separation on a denaturing gel. Afterannealing of the respective 3′ ends, the oligonucleotides were extendedwith DNA polymerase to form a 100 bp double-stranded DNA fragment.Following restriction with SacI and KpnI, the random fragments wereligated to pET23d:HSVTK-Dummy, which is described above and by Black etal., Proc. Nat'l Acad. USA 93:3525-3529, 1996). Vectors containing themix of random sequences were used to transform a thymidinekinase-deficient E. coli, and the transformed E. coli were plated ongrowth medium which requires the presence of a functional plasmid-borneTK. A total of 120 clones were picked and restreaked onto selectivemedium to confirm the phenotype. Individual colonies were used toinoculate selective medium aliquoted in 96-well plates (one clone/well).Cultures were examined for their sensitivity to different levels of GCVor ACV. Lysates of all 120 mutants were assayed for the ability tophosphorylate thymidine, ACV and GCV, using methods described above.

Seven mutants that demonstrated required activities were selected forfurther study. Table VI shows the deduced amino acid sequence of theseseven mutants (SR11, SR26, SR39, SR4, SR15, SR32, SR53).

TABLE VI Amino Acid Substitutions at  Residues 159-161 and 168-169 in Second Generation  Semi-Random Mutants wild-type TK LIFDRHPIAALL SR11-FL FN SR26 -FA F- SR39 IFL FM SR4 ILL YL SR15 -FA YY SR32 -FV VM SR53IFV FY

B. Analysis of Second Generation TK Mutants

1. In Vitro Analysis of Second Generation Semi-Random Mutants in CellLines

The seven mutants were subcloned into the mammalian expression vector,pREP8D7:dualGFP. This vector contains a constitutive metallothioninpromoter, which drives the expression of green flourescent protein(GFP), and an RSV LTR promoter, which stimulated expression of the TKmutants. The vector also contains a histidinol resistance gene forselection of transformants. Purified vector DNA of these constructs wasused to transfect BHK tk-cells by electroporation. The transfectantswere selected by resistance to histidinol and sorted using FACS analysisfor GFP expression. Pools of transfectants were then assayed forsensitivity to GCV or ACV over a range of prodrug doses. In both ACV andGCV assays, six of the seven mutants revealed lower IC₅₀ values than thewild-type TK transfectant pool. The remaining mutant transfectant pool(SR53) expressed low levels of TK protein which may account for itslower prodrug sensitivity. The results presented in Table VII show thatmutants SR11, SR26, and SR39 are superior to wild-type TK or to mutant75, using ACV as a substrate. Table VIII illustrates the IC₅₀ valuesfrom Rat C6 kill curves with the SR11, SR26, and SR39 mutants.

2. In Vivo Analysis of Second Generation Semi-Random Mutants in an InVivo Mouse Xenograft Tumor Model

Rat C6 glioblastoma cells were transfected with the stable expressionvector pREP8D7:dualGFP as described above containing various TK mutants.Cells were transfected with either WT, SR39 or mutant 30 (LIF-ALLseries) and sorted for comparable levels of GFP expression. Experimentswere carried out to establish prodrug dosing levels for tumor ablationand efficacy of therapy. Nude mice (JAX Labs, Bar Harbor, Me.) wereinjected subcutaneously with 0.5×10⁶ transfected rat C6 cells. After 5days, prodrugs (ACV and GCV) were administered twice a day for a further5 days. Prodrug was given at either of two concentrations (shown asmg/kg). During this period and for an additional 6 days, tumor size wasmonitored by caliper measurement every other day. At the end of theperiod, mice were sacrificed and the tumors excised and weighed.

Data is presented in FIGS. 32, 33 (tumor diameter) and 34 (final tumorweight) and demonstrates that SR39 (as well as mutant 30) is a highlyeffective mutant and can cause significant tumor reduction using eitherACV or GCV. The degree of in vivo tumor inhibition using both mutant 30and SR39 are clearly superior to that of the wild-type enzyme. Further,data with SR39 and ACV suggest for the first time that ACV can functionas an effective prodrug for suicide gene therapy.

TABLE VII ICSO Values for ACV Kill Curves Enzyme ACV (μM) TK 0.2 75 0.06SR11 0.025 SR26 0.035 SR39 0.03

TABLE VIII IC₅₀ Values from Rat C6 Kill Curves IC₅₀ (μM) relative torelative to GCV TK ACV TK TK 5 1 >20 1  30 0.01 500 0.26 >77  75 >1<5 >20 — 411 0.1 50 14 >1.4 SR11 0.15 33 6 >3 SR26 0.04 125 0.76 >26SR39 0.107 294 0.11 >182

Enzyme kinetic analyses of purified SR11, SR26, and SR39 proteins wereperformed as described above. The results of these studies aresummarized in Table IX.

TABLE IX Kinetics of Semi-Random Library Mutants Km (μM) Thymidine GCVACV TK 0.4 47 319 SR11 1.0 6.4 5.6 SR26 1.4 17.6 3.4 SR39 6.7 3.3 9.8

Example 10 Mutagenesis of a Region within the Q Substrate Binding Domainof HSV-1 Thymidine Kinase

This example describes the construction and analysis of TK mutants thathave been mutagenized in a region of the recently identified Q substratebinding domain.

A. Isolation of TK Mutants having Modifications in the Q SubstrateBinding Domain

To construct a dummy vector for insertion of the random sequences, aNarI (or KasI) site was introduced into pET23d:HSVTKII by site-directedmutagenesis, using primer DM01358 (5′-GTCTCGGAGGCGCCCAGCACC-3′) withinthe wild-type thymidine kinase open reading frame at nucleotide position276 from the ATG. The pET23d:HSVTKII vector is described by Black etal., Proc. Nat'l Acad. Sci. USA 93:3525-3529, 1996. Restriction ofpET23d:HSVTK-Nar, which is the pET23d:HSVTKII vector with an engineeredNarI site, by SacI and NarI allowed removal of TK sequences andreplacement by a 1 kb NarI/SacI fragment from the vector, pLXSN. Thisvector was designated pET23d:HSVTK-Nar Dummy.

For the first random library, two oligonucleotides were synthesizedcontaining the three non-wild-type nucleotides at a frequency of 9%(i.e., the wild-type nucleotides were represented at 91% frequency) forthe codons corresponding to residues 112-132. FIG. 22 shows thesequences of oligonucleotides DMO-1860 and -1861, which arecomplementary and overlap. These oligonucleoties represent wild-typesequences. Random mutations were introduced by including non-wild-typenucleotides at a frequency of 9% for synthesis of regions presented inboldface type of DMO-1860 and -1861 oligonucleotides (i.e., after thediscontinuity indicated in each sequence). FIG. 22 also outlines how theoligonucleotides were used in a PCR amplification to generate thecorrect-sized fragment. Briefly, an initial set of polymerase chainreactions (20 rounds) was performed to combine the four internaloligonucleotides (DMO-1860, DMO-1861, DMO-1893, and DMO-1894) intofull-length product. A second PCR set (10 rounds) used the two smalleroligonucleotides, designated DMO-1895 and DMO-1896, to amplify theproduct and to add overhanging sequences for restriction cleavage. Theproduct of this reaction was cleaved with KasI and SacI and ligated intothe pET23d:HSVTK-Nar Dummy (KasI/SacI) vector. Following electroporationinto BL21(DE3) tdk-E. coli, the cells were plated onto TK selectionplates and scored for growth. All colonies were retested on fresh TKselection plates. Several hundred clones were sequenced and found tocontain zero to six amino acid substitutions spanning the 20 amino acidregion.

Two subsequent libraries were constructed using only one of themutagenic oligonucleotides to increase the frequency of single aminoacid changes. Several hundred TK positive clones were sequenced. Lysatesfrom these mutants have been assayed for the ability to phosphorylatethymidine, acyclovir and ganciclovir, demonstrating that mutation withinthe Q substrate binding domain alters substrate specificity.

Example 11 Isolation of Human and Mouse Guanylate Kinases andConstruction of HSV-1 Thymidine Kinase and Guanylate Kinase DualExpression Vectors

This example describes the isolation of the human and mouse guanylatekinase genes and the vector construction for dual expression of herpesthymidine kinase and guanylate kinase.

A. Isolation of the Human Guanylate Kinase Gene

1. Isolation of the Human Guanylate Kinase Gene

Two oligonucleotides are designed to amplify the entire human guanylatekinase open reading frame. The following two oligonucleotides aresynthesized by GenSet (La Jolla, Calif.):5′-ACTACTGGAT[CCATGG]CGGGCCCCAGGCCTGTG-3′, a 33-mer (SEQUENCE ID. NO.26) and 5′-TACTACGGATCCTCAGGCGGCGGTCCTTTGAGC-3′, a 33-mer (SEQUENCE ID.NO. 27). The BamHI sites at each end are underlined and the Ncol site atthe initiating methionine codon is shown in brackets. The boldnucleotide denotes a nucleotide alteration from the original sequence(GenBank accession number A11042). The human guanylate kinase gene isamplified from a cDNA library of human proliferating B lymphocytesstimulated with alpha-CD3. The resulting single band (˜600 bp) isrestricted with BamHI and cloned into pUC118 (BamHI) to yieldpUC118:Hugmk. The insert is sequenced in entirety (both strands) usingthe following set of oligonucleotides: 5′-CTGCTGAAGAGGCTGCTC-3′ (18 mer)(DMO 512) (SEQUENCE ID. NO. 28), 5′-ACACAGATGCGGTTTCATG-3′ (19 mer) (DMO513) (SEQUENCE ID. NO. 29), 5′-CTGGACGTGGACCTGCAG-3′ (18 mer) (DMO 514)(SEQUENCE ID. NO. 30), 5′-GTTAATGATGACCACATC-3′ (18 mer) (DMO 515)(SEQUENCE ID. NO. 31), 5′-TGTAAAACGACGGCCAGT-3′ (18 mer) (M13 forwardprimer purchased from ABI) (SEQUENCE ID. NO. 32) and5′-CAGGAAACAGCTATGACC-3′ (18 mer) (M13 reverse primer from ABI)(SEQUENCE ID. NO. 33). Sequence analysis revealed identity with theGenBank sequence except for the anticipated alteration at the NcoI sitewhich results in a serine to alanine change (S2A) (FIG. 24).

2. Northern Blot

8 μg of total RNA from SP2/0 murine B lymphoma cells is prepared in 1×MOPS buffer/75% formamide and heat denatured for 10 min at 55° C. andloaded on a 1.2% agarose gel in 1× MOPS buffer. After transfer tonitrocellulose the blot is probed with the human gmk gene.

The 600 bp BamHI fragment is gel isolated from pUC118:Hugmk and islabeled using the random primer labeling kit from Amersham according tothe manufacturer's instructions. The free radiolabel is removed by sizeexclusion chromatography. Following hybridization and washes the blot isexposed to X-ray film at −70° C. for two days. Autoradiography of thenorthern blot reveals a single −750 nt RNA species. In a similarexperiment using human poly A+ RNA from proliferating B lymphocytes, asingle −750 nt band is also observed.

B. Isolation of Mouse Guanylate Kinase Gene

1. Screening a Mouse cDNA Library

A lambda gt10 cDNA library of mouse 702/3 cells (B lymphomas) is probedusing the human gene (same probe as used for northern blot analysis).The total number of plaques screened is 2×10⁵ pfu. Nine independentlambda clones hybridized to the human probe and are plaque purified.

2. Subcloning and Sequence Analysis of Positive Clones

The EcoRI fragments from eight phage DNA preparations are gel isolatedand subcloned into pUC118 restricted with EcoRI and dephosphorylated.The DNA insert sizes ranged from ˜300 bp to 1.2 kb. Preliminary sequenceanalysis with primer (M13 forward primer) reveals that all clones beganapproximately 60 bp 5′ to the putative ATG start codon as determined bysequence alignment with the human and bovine guanylate kinase sequencesand varied at their respective 3′ ends. One representative clone (bothstrands) is completely sequenced using the following oligonucleotides:5′-TGTGTCCCATACTACTACAAG-3′ (21 mer) (DMO 592) (SEQUENCE ID. NO. 34),5′-TGAGAACTCAGCAGCATGCTC-3′ (21 mer) (DMO 594) (SEQUENCE ID. NO. 35),5′-GTGCTAGATGTCGACCTA-3′ (18 mer) (DMO 595) (SEQUENCE ID. NO. 36),5′-ACCTGGATAAAGCCTATG-3′ (18 mer) (DMO 674) (SEQUENCE ID. NO. 37),5′-AAGCAGGCGCTCTCTCTGA-3′ (19 mer) (DMO 675) (SEQUENCE ID. NO. 38),5′-CTATTTCTCATATGATGT-3′ (18 mer) (DMO 731) (SEQUENCE ID. NO. 39) and5′-GTTACAGTGTCTCTAGAG-3′ (18 mer) (DMO 732) (SEQUENCE ID. NO. 40),5′-TCCCCCACCTCCAGGC-3′ (16 mer) (DMO 748) (SEQUENCE ID. NO. 52),5′-CTCAGTGTTGCCCAGTCG-3′ (18 mer) (DMO 749) SEQUENCE ID. NO. 53) and5′-GCCGAAGATGCTGCTGTG-3′ (18 mer) (DMO 750) SEQUENCE ID. NO. 54). Thefinal murine guanylate kinase gene sequence is shown in FIG. 25 with thededuced amino acids.

3. Introduction of a New Restriction Site

A novel NcoI restriction site is introduced at the start codon of themouse guanylate kinase open reading frame as described in Black, M. E.and Hruby, D. E. (J. Biol. Chem. 265:17584-17592, 1990). The mutagenicoligonucleotide used is: 5′-CTAGGTCCTG[CCATGG]CGTCCGCG-3′ (24 mer) (DMO676) (SEQUENCE ID. NO. 41) with the NcoI site shown in brackets and thebold nucleotide denoting a C to G change. The resulting clone,pUC118:Mugmk-NcoI, is sequenced to confirm orientation and the 5′junction region.

C. Construction of Vectors for In Vitro Transcription and TranslationAnalysis

Both the human and murine guanylate kinase genes are subcloned intopET23d (see Example 8). The 600 bp NcoI/BamHI fragment from pUC118:Hugmkis gel isolated and directionally subcloned into pET23d (see Example 8)restricted with NcoI and BamHI. The murine guanylate kinase gene is gelisolated as a ˜800 bp NcoI/EcoRI fragment using the introduced NcoI siteat the ATG and the EcoRI site from the pUC118 3′ polylinker region, andcloned into pET23d (see Example 8) restricted with NcoI and EcoRI. Theresulting plasmids, pET23d:Hgmk and pET23d:Mgmk, are then used astemplates for in vitro transcription and, the mRNAs produced, are usedin a rabbit reticulocyte lysate cell free translation system asdescribed in Examples 3 and 8. Enzyme assays to confirm full-lengthprotein production and activity are as described in Agarwal et al.(Methods in Enzymol. 51:483⁻490, 1978) with bovine guanylate kinasepurchased from Sigma as a positive control.

D. Purification and Characterization of the Human and Mouse CivanylateKinases

1. Expression Vector Construction

The pET23d vector (Novagen, Madison, Wis.) is used as the vectorbackbone for the construction of pET:HT. This vector contains a 6histidine residue peptide followed by a thrombin cleavage site to allowfor the expression of a removable histidine tag fused to the N terminusof the target gene product. Synthesis of the 6 his-thrombin fusionencoding region is done by PCR amplification of the promoter region ofpET23d and extension using the following primers in three sequential PCRamplification steps. 5′-ACTACTACTA GATCTCGATC CCGCGAA-3′ (27 mer) (DMO604) (SEQUENCE ID. NO. 42) 5′-ATGATGATGA TGATGGCTGC TAGCCATAGTATATCTCCTT C-3′ (41 mer) (DMO 605) (SEQUENCE ID. NO. 43) 5′-CGGCACCAGGCCGCTGCTGT GATGATGATG ATGATGGCT-3′ (39 mer) (DMO 606) (SEQUENCE ID. NO.44), 5-AGTAGTAT[CC ATGG]AGCTGC CGCGCGGCAC CAGGCCGCTG CT-3′ (42 mer) (DMO607) (SEQUENCE ID. NO. 45). Sequence DMO 604 is annealed to the BglIIregion of pET23d in all PCR amplification steps. Sequence DMO 605 isannealed to the region corresponding to the NcoI site in a 3′ to 5′orientation and results in the loss of the NcoI site due to a nucleotidemutation shown in bold in the sequence above. Subsequent amplificationswith sequence DMO 606 or DMO 607 in the 3′ to 5′ orientation are pairedwith sequence DMO 604 to extend the sequence for the addition of 6histidine codons and a thrombin cleavage site. A new NcoI site is alsointroduced with sequence DMO 607 as shown in brackets above. The finalBglII/NcoI fragment is cloned into pET23d at the corresponding sites tocreate pET:HT. pET:HT is sequenced to confirm correct synthesis andinsertion. The amino acid sequence of the new vector fusion peptide is:MA S S H H H H H H S S G L V P R G S S M (NcoI site) (SEQUENCE ID. NO.46) with the thrombin cleavage recognition site underlined. Cleavagewith thrombin is between the arginine and glycine residues.

2. Overexpression in E. coli and Affinity Purification

Methods for overexpression and analysis are as in Example 8. Affinitypurification using His-Bind Resin (Novagen, Madison Wis.) is performedaccording to the manufacturer's instruction. Thrombin is used to cleaveoff the terminal 17 amino acids to leave three amino acids N-terminal tothe guanylate kinase initiating methionine. The leader peptide is thenremoved by passing the cleavage mix over the His-Bind column a secondtime.

3. Enzyme Kinetics

The K_(m), V_(max) and K_(cat) values for guanylate, GCV-monophosphateand acyclovir-monophosphate are determined using purified human andmouse guanylate kinases. In addition to using the assay protocoldescribed in Agarwal et al. (Methods in Enzymol. 51:483-490, 1978), thenucleotide products generated from assays performed with radionucleotidesubstrates are analyzed by thin layer chromatography and scintillationcounting.

E. Expression of Human and Murine Guanylate Kinases in Mammalian Cells

1. Vector Construction

Both human and murine guanylate kinase genes are cloned into a modifiedpREP8 vector. Briefly, for construction of the modified pREP8 (pREP8-7kb), pREP8 (Invitrogen) is digested with BstEII and XbaI, filled in withKlenow and religated. The resulting plasmid, pREP8-7 kb, no longerencodes EBNA-1 or the EBV origin of replication (oriP). Both guanylatekinases, pET23d:hgmk and pET23d:mgmk (described above) are restrictedwith NcoI, blunt-ended and then digested with BamHI to yield a −600 bpNcoI (blunt)-BamHI fragment after gel purification. These are ligated topREP8-7 kb that has been digested with HinDIII (blunt-ended) and BamHI.The new plasmids are designated pREP8-7:hgmk and pREP8-7:mgmk.

2. Isolation of Stable Transfectants Expressing HSVTK

BHKtk-(ts13) cells are transfected with pCMV, pCMV:TK, pCMV:30 andpCMV:75 DNA in the presence of pSV2-neo (10:1 ratio) as described inExample 8. Approximately 10-20 individual clones from each pCMV DNAtransfection are isolated under 1 mg/ml G418 selection. As in example 8,about 2×10⁶ cells per clone are examined for TK expression level bywestern blot using polyclonal anti-TK serum.

Expression of TK clone C3 is very high, whereas 75 D4 and 30 A2 are lessthan half the TK expression level of C3. 75 D2, D3 and D4 proteinexpression ranged from very low, low to moderate, respectively.

3. Sensitivity of Clones to GCV or ACV

Clones are assayed for sensitivity to GCV and ACV as described inExample 8. Sensitivity to GCV and ACV is dependent on the level ofprotein expression. This can clearly be seen with the 75 clones, D2, D3and D4 where the highest expression clone D4 is the most sensitive, D3is less so and D2 is even less sensitive than D3 to prodrugs. (FIGS. 26,27)

4. Transfection of TK-Expressing Cells with pREP8-7 Guanylate KinaseConstructs

pREP8-7, pREP8-7:hgmk and pREP8-7:mgmk are used to transfect BHK tk,TK-transfected clone C3 and 75-transfected clone D4. Histidinol is usedto select pools of stable transfectants and to isolate individualclones.

Protein expression levels of guanylate kinase in the different pools isdetermined by immunoblot analysis. Briefly, 5 μl of 2×10⁶ cell pelletlysates (200 μl) are subjected to electrophoresis and transferred tonitrocellulose. Polyclonal anti-guanylate kinase serum (at a 1:5,000dilution) and TK antiserum (at a 1:10,000 dilution) is utilized todetect the resultant protein bands.

5. Sensitivity of Guanylate Kinase Transfectant Pools to GCV and ACV inTK Expressing Clones

As in Example 8, pools of transfectants are placed in 96 well microtiterdishes at 1000 cells/well. Eight replicates are incubated for three daysin the presence of various GCV or ACV concentrations.

As can be seen in FIGS. 28 and 29, the level of prodrug sensitivity isrelated to the level of TK protein expression and the presence ofguanylate kinase. Guanylate kinase expression in the presence ofwild-type TK demonstrates approximately 2 fold increased sensitivity toACV relative to TK expression alone. Despite half the expression levelof wild-type TK, sensitivity to ACV by gmk+75 D4 expressing cells is 6-7times greater than that of TK expressing cells.

F. Construction and Analysis of Dual Expression Vectors In Vivo

The HSV1 tk gene is cloned into the HpaI site of pLXSN (Miller andRosman, BioTechniques 7:980-990, 1989) as a NcoI (blunt-ended) fragmentand the orientation determined by restriction mapping. This places theHSV-1 tk gene behind the MoMLV LTR promoter. The neomycinphosphotransferase gene is replaced by the guanylate kinase gene (humanor mouse) as a BamHI (blunt-ended) fragment such that guanylate kinasegene expression is driven off the SV40 promoter. In addition, vectorsare constructed where the tk and gmk gene order is reversed such thatthe tk gene is expressed from the SV promoter and gmk is expressed fromthe LTR promoter. Vector constructs with individual genes (tk or gmk)are also constructed. Furthermore, expression vectors containing HSV-1tk mutants in place of the wild-type HSV-1 tk genes are alsoconstructed.

As in Example 8, plasmid DNA from the constructs described above areused to transfect ts13 BHK tk-cells, SF767 human glioblastoma cells, andrat C6 glioblastoma cells in the presence of a marker plasmid (pSV2-neo)to enable the selection of transfectants on G418.

Selection of stable transfectants and assays for increased sensitivityto ACV and GCV are as described in Example 8.

Example 12 Construction and Analysis of Guanylate Kinase-ThymidineKinase Fusion Proteins

This example illustrates the production and analysis of several fusionproteins that have both guanylate kinase and thymidine kinaseactivities.

A. Construction of Fusion Proteins

Use of a fusion protein for gene therapy would not only negate therequirement for two promoters and the associated reduction in prodrugactivation due to the differences in promoter strength, it would alsoallow expression of two enzyme functions from a single promoter and asingle cistron. Accordingly, fusion proteins are advantageous for genetherapy vectors which cannot tolerate large pieces of foreign DNA, suchas AAV vectors.

Two fusion proteins have been constructed that contain both wild-typeHSV-1 TK and murine guanylate kinase (gmk) sequences. These proteinsdiffer in the number of residues at the fusion site. Both fusionconstructs can be over-expressed in E. coli from pET23d backbonevectors. In both vectors, guanylate kinase was located adjacent to thepromoter with TK fused to the MscI site at the 3′ end of gmk whichremoves the two C-terminal amino acids. One fusion was constructed suchthat the first nine amino acids of TK are absent (pET23d:gmk/TK-trunc).The other fusion contains the entire TK amino acid sequence(pET23d:gmk/TK-fl). Maps of these constructs are illustrated in FIG. 30.

Six additional fusion proteins have been constructed in which thewild-type TK sequence of pET23d:gmk/TK-fl is replaced by TK mutant 30,mutant 75, mutant 411, SR11, SR26 or SR39 sequences. These fusionproteins were over-expressed in BL21(DE3) tk-cells.

B. Analysis of Fusion Proteins

All of the above constructs were cloned into pREP8D7:dualGFP, asdescribed above. These vectors were used to transfect BHK tk-cells andtransfectants were selected on the basis of resistance to histidinol.Further screening for GFP expression was performed by FACS analysis. Inaddition, the gmk/TK-fl construct was used to transfect rat C6 gliomacells and positive clones/pools were selected as described above. Aganciclovir dose response curve comparing gmk/TK-trunc to wild-type TKin rat C6 cells is shown in FIG. 31. This curve demonstrates a 100-folddifference in IC₅₀ between the two enzymes with the fusion protein beingthe superior one.

Both wild-type TK-gmk fusion proteins were over-expressed in E. coli andpurified to homogeneity using affinity chromatography. Michaelis-Mentenkinetics for both thymidine kinase and guanylate kinase activities wereexamined with both fusion proteins, and the results are shown in TableX. The thymidine kinase activity is similar to wild-type levels.However, gmk function is impaired 3.8 to 5.8 fold in the fusion proteinconstructs compared to wild-type gmk. Nevertheless, the fusion proteinsexhibited both guanylate kinase and TK activities.

TABLE X Kinetic Analysis of Fusion Proteins Km (μM) gmk gmk/TK-trunkgmk/TK-fl TK GMP 25 95 146 — dGMP 218 359 — thymidine — 0.67 0.5 0.3

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

1-15. (canceled)
 16. An isolated nucleic acid molecule encoding a fusionprotein comprising a guanylate kinase moiety and a thymidine kinasemoiety, wherein said fusion protein possesses a biological activity ofguanylate kinase and a biological activity of thymidine kinase, whereinsaid thymidine kinase moiety is either a Herpesviridae thymidine kinaseor a mutant Herpesviridae thymidine kinase that possesses an increasedbiological activity, compared with unmutated thymidine kinase.
 17. Theisolated nucleic acid molecule according to claim 16, wherein at leastone of said guanylate kinase moiety and said thymidine kinase moiety istruncated.
 18. The isolated nucleic acid molecule according to claim 16,wherein said guanylate kinase moiety is a mammalian guanylate kinase.19. The isolated nucleic acid molecule according to claim 18, whereinsaid mammalian guanylate kinase moiety is a murine guanylate kinase or ahuman guanylate kinase.
 20. The isolated nucleic acid molecule accordingto claim 16, wherein said mutant thymidine kinase is an enzymecomprising one or more mutations, at least one of said mutationsencoding an amino acid substitution located toward the N-terminus from aDRH nucleoside binding site.
 21. The isolated nucleic acid moleculeaccording to claim 16, wherein said mutant thymidine kinase is an enzymecomprising one or more mutations, at least one of said mutations beingan amino acid substitution within a DRH nucleoside binding site.
 22. Theisolated nucleic acid molecule according to claim 16, wherein saidmutant thymidine kinase is an enzyme comprising at least threemutations, at least two of said mutations encoding amino acidsubstitutions that are located one, two or three amino acids toward theN-terminus from a DRH nucleoside binding site, and at least one of saidmutations encoding an amino acid substitution that is located four orfive amino acids toward the C-terminus from a DRH nucleoside bindingsite.
 23. The isolated nucleic acid molecule according to claim 20,wherein said mutant thymidine kinase is an enzyme comprising at leastone mutation in the Q substrate binding domain.
 24. The isolated nucleicacid molecule according to claim 16, wherein said thymidine kinase isselected from the group consisting of Herpes Simplex Virus Type 1thymidine kinase and Herpes Simplex Virus Type 2 thymidine kinase. 25.An expression vector comprising the isolated nucleic acid molecule ofclaim
 16. 26. The expression vector of claim 25 further comprising apromoter operably linked to said nucleic acid molecule. 27-60.(canceled)